supplementary information for: signals of recent positive
TRANSCRIPT
Supplementary information for: Signals of recent positive selection
in a worldwide sample of human populations
Joseph K. Pickrell1,†, Graham Coop1,12,†, John Novembre1,2,
Sridhar Kudaravalli1, Jun Li10, Devin Absher4, Balaji S. Srinivasan6,7,8,9,
Gregory S. Barsh3, Richard M. Myers4, Marcus W. Feldman5,
and Jonathan K. Pritchard1,11,†
1 Department of Human Genetics, The University of Chicago.2 Department of Ecology and Evolutionary Biology, UCLA.
3 Department of Genetics, Stanford University.4 HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL.
5 Department of Biological Sciences, Stanford University.6 Stanford Genome Technology Center, Stanford University7 Program in Biomedical Informatics, Stanford University
8 Dept. of Computer Science, Stanford University9 Dept. of Statistics, Stanford University
10 Dept. of Human Genetics, University of Michigan11 Howard Hughes Medical Institute.
12 Current Address: Department of Ecology and Evolution, University of California, Davis
† To whom correspondence should be addressed: [email protected],
[email protected], [email protected]
January 12, 2009
1
Power simulations. To estimate our power to detect selection in the ascertained Illuminadata, we performed simulations under the “cosi” model of human demography [3] with a slightmodification– for computational efficiency, the recent increases in population size were dropped.This had little effect on the fit of the model to the HapMap data (results not shown). Other rele-vant parameters are described in the main text. The selection model is one where a single selectedsite arises and sweeps up in frequency. Implicitly, this assumes a given selected locus in the humangenome has experienced only a single selective sweep in the time from over which our statisticsare applicable (approximately 10-80ky); we find this reasonable, and simulations of this kind are astandard method for testing the power of a test for selection [2, 4–7]
To approximate the ascertainment of the Illumina panel, we performed a two-stage ascertain-ment on all of the simulations; this is described in the main text. In Supplementary Figure 1, weshow that this procedure provides a good approximation to the frequency spectrum of the Illuminachip. For calculations of power, in all cases the selected site was excluded from analysis, makingthe calculations conservative. In Supplementary Figure 2, we show power estimates as a functionof derived allele frequency in different demographies, and in Supplementary Figure 3, we show theeffect of sample size on power.
About 200 of the simulations have a selected allele that arises on the branch common to boththe “European” and “Asian” populations; this allows us to get an upper bound on the expectedamount of overlap between the populations for XP-EHH (with a selection coefficient of 1% almostall selected alleles that arose during that branch would have gone to fixation and are not likely tobe detected by iHS). In these simulations of truly shared selective sweeps, 76% are detected in bothpopulations.
Overlap of haplotype-based selection signals between populations. We calculated iHSand XP-EHH in each individual population, and converted scores to empirical p-values as describedin the text. For a signal to be considered overlapping between populations, we required that theiHS or XP-EHH score be in the 1% tail of one population and the 5% tail of the other. InSupplementary Figures 4 and 5, we show the fraction of selection signals that overlap betweenall pairs of populations. The striking difference between African and non-African populations inXP-EHH is an artifact of the way XP-EHH is calculated–for non-African populations, we used thegroup of Bantu speakers as a reference, and for African populations we used a group of Europeanchromosomes as the reference. We performed the test this way to most closely follow what was mostpowerful in the simulations, but this means that the non-overlap between African and non-Africanpopulations by XP-EHH is not meaningful.
Calculation of the CLR statistic and overlap with other signals of selection The CLRtest used in the main text as an alternative to XP-EHH for detecting high-frequency sweeps wasoriginally designed to be applied to data for which SNP ascertainment is constant across the genomeand, ideally, can be properly modeled. This is not the case for the HGDP data–tag SNPs wereidentified in the HapMap database, which has complicated and often unknown ascertainment [1].
2
Because of this, we have used this statistic not as a formal test for significance, but rather to rankregions by the deviance of the allele frequency spectra from the genome-wide average. We then usedthe CLR statistics as test statistics like XP-EHH and iHS and convert them to empirical p-valuesafter controlling for SNP density, as described in the main text.
As XP-EHH and CLR both detect local deviations in the allele frequency spectrum (XP-EHHdetects regions of extended homozygosity), we expect them to largely overlap. This is indeed thecase for non-African populations–defining overlap as above, we find that the CLR and XP-EHHstatistics overlap 63%, 58%, 67%, 83%, 88%, and 71% for Europe, the Middle East, S. Asian, E.Asia, Oceania, and the Americas, respectively. For the Bantu, however, the overlap is only 28%.We interpret this to mean that many signals of fixed sweeps in the Bantu are less robust thanthose outside of Africa. This is consistent with the observation that there appear to be few reliablesignals of recent fixations in African populations[2, 4].
3
0 1 0 1 0 1
Derived allele frequency
Den
sity
AS
NY
RI
CE
U
Unascertained simulations Ascertained simulations Illumina
Figure 1: Marginal frequency spectra in the simulations before and after the application of theascertainment procedure, as well as in the real data. In the first column are the marginal allelefrequency spectra in the simulations before application of the ascertainment procedure, in thesecond column are the allele frequency spectra in the simulations after the application of theascertainment procedure, and in the third column are the marginal allele frequency spectra in theHapMap populations at the SNPs typed on the Illumina panel.
4
0.2 0.4 0.6 0.8 1.0
0.0
0.2
0.4
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Derived allele frequency
Po
we
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0.0
0.2
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Derived allele frequency
Po
we
r
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CEU
ASN
A B
Figure 2: Power of iHS (A) and XP-EHH (B) in three demographies based on theHapMap. Selected alleles were introduced at a random time with a selection coefficient of 1%and simulated forwards in time. In all simulations, the selected site was excluded from analyses.Simulations were binned into six bins according the the final frequency of the selected allele. Thetype I error was set to 1%, with the threshold determined by neutral simulations.
5
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0.0 0.2 0.4 0.6 0.8 1.0
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BA
Figure 3: Power of iHS (A) and XP-EHH (B) in the YRI demography for differentsample sizes (in number of chromosomes). Selected alleles were introduced at a random timewith a selection coefficient of 1% and simulated forwards in time. Simulations were binned into sixbins according the the final frequency of the selected allele. The type I error was set to 1%, withthe threshold determined by neutral simulations.
6
BantuKenya
BantuKenya
BantuSouthAfrica
BantuSouthAfrica
Yoruba
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San
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Figure 4: Overlap of iHS signals across populations. In each cell (i, j) the fraction of windows withscores in the 1% tail of iHS in population i and in the 5% tail of iHS in population j is coloredaccording the legend on the right.
7
BantuKenya
BantuKenya
BantuSouthAfrica
BantuSouthAfrica
Yoruba
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San
San
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Figure 5: Overlap of XP-EHH signals across populations. In each cell (i, j) the fraction of windowswith scores in the 1% tail of XP-EHH in population i and in the 5% tail of XP-EHH in populationj is colored according the legend on the right.
8
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pe
Mid
east
S.A
sia E.A
sia Oce
ania
Am
erica
0.0
5
0.0
01
Figure 6: Top 10 iHS (A) and XP-EHH (B) signals by population cluster. This isanalogous to Figure 1 in the main text, but uses a sliding window of 200kb that slides in steps of100kb.
9
chr9
31.
2:31
.6ch
r7 6
6.6:
67ch
r2 9
7.6:
97.8
COX5
B,AC
TR1B
,ZAP
70ch
r5 1
09:1
09.2
MAN
2A1
chr6
26.
4:26
.6BT
N3A2
,BTN
2A2,
BTN3
A1,B
TN2A
3,BT
N3A3
,BTN
2A1
chr3
29.
4:29
.8RB
MS3
chr1
1 57
.8:5
8O
R5B1
7,O
R5B3
,OR5
B2,O
R5B1
2ch
r3 1
33.2
:133
.4CP
NE4
chr6
85.
4:85
.6TB
X18
chr1
3 35
.4:3
5.6
DCAM
KL1
chr1
9 43
.4:4
3.6
DPF1
,PPP
1R14
A,SP
INT2
,LO
C541
469,
C19o
rf33,
YIF1
B,KC
NK6,
C19o
rf15,
PSM
D8,G
GN,
SPRE
D3,R
ASG
RP4,
FAM
98C
chr9
11.
8:12
chr1
1 10
9.8:
110.
2FD
X1,A
RHG
AP20
chr1
4 97
.6:9
7.8
chr1
0 20
.4:2
0.6
PLXD
C2ch
r11
9.8:
10.2
SBF2
chr9
99.
6:99
.8AN
P32B
,C9o
rf156
,FO
XE1,
HEM
GN
chr1
6 22
.8:2
3HS
3ST2
,USP
31ch
r4 1
19.8
:120
KIAA
1627
,SEC
24D
chr2
167
.6:1
68CM
YA3
chr1
7 60
.6:6
0.8
RGS9
chr9
107
:107
.2SL
C44A
1ch
r14
60.8
:61.
2TM
EM30
B,PR
KCH
chr4
60.
6:61
chr9
3.2
:3.4
RFX3
chr3
131
.4:1
31.8
FLJ3
5880
chr3
25.
8:26
OXS
Mch
r2 1
78:1
78.2
AGPS
,TTC
30A,
TTC3
0B,P
DE11
Ach
r2 2
12.8
:213
.2ER
BB4
chr4
34:
34.2
chr1
4 62
.6:6
3KC
NH5,
RHO
J,G
PHB5
,PPP
2R5E
chr5
19.
6:20
CDH1
8ch
r8 1
39.6
:139
.8CO
L22A
1ch
r15
27:2
7.2
APBA
2ch
r7 1
19.8
:120
.2KC
ND2
chr1
5 46
:46.
4SL
C24A
5,M
YEF2
,SLC
12A1
chr1
7 51
:51.
4TM
EM10
0,PC
TPch
r8 1
1:11
.2C8
orf1
5,M
TMR9
,XKR
6ch
r22
45:4
5.2
FLJ2
0699
,PPA
RA,L
OC1
5038
3,PK
DREJ
,GTS
E1,T
RMU,
CELS
R1ch
r10
83.8
:84.
2NR
G3
chr6
73.
8:74
KCNQ
5ch
r2 1
08.8
:109
FLJ3
2745
,EDA
Rch
r6 1
25.8
:126
.2HE
Y2,N
COA7
chr2
108
:108
.4SU
LT1C
3,SU
LT1C
1,SU
LT1C
2ch
r10
55.6
:55.
8PC
DH15
chr1
0 94
.8:9
5.2
EXO
C6,C
YP26
C1,C
YP26
A1,F
ER1L
3ch
r5 1
12.2
:112
.6AP
C,SR
P19,
DCP2
,MCC
,REE
P5ch
r10
55:5
5.2
chr1
1 25
.2:2
5.6
chr1
2 1.
2:1.
4ER
C1ch
r8 6
3.8:
64FA
M77
Dch
r3 6
7.6:
67.8
SUCL
G2
chr2
165
.2:1
65.6
COBL
L1,F
LJ39
822
chr2
126
:126
.2ch
r14
69.4
:69.
6SM
OC1
,SLC
8A3
chr5
61.
2:61
.4ch
r6 2
9.4:
29.6
OR5
V1,O
R12D
3,O
R12D
2,O
R11A
1,O
R10C
1,O
R2H1
,MAS
1Lch
r3 1
62.6
:162
.8LO
C131
149
chr1
2 92
.8:9
3ch
r2 1
65.8
:166
.2SC
N2A,
FAM
130A
2ch
r16
11:1
1.4
PRM
1,KI
AA03
50,S
OCS
1,TN
P2,P
RM3,
PRM
2,C1
6orf7
5ch
r2 1
61.2
:161
.6ch
r6 4
7.6:
47.8
GPR
115,
GPR
111,
CD2A
Pch
r10
110:
110.
2ch
r12
30.8
:31
TSPA
N11
chr6
122
.6:1
22.8
HSF2
chr1
3 87
.8:8
8.2
chr5
141
:141
.2C5
orf1
6,FC
HSD1
,CEN
TD3
chr4
68.
6:68
.8TM
PRSS
11F,
CHR4
15SY
T,TM
PRSS
11B
chr8
33.
4:33
.6FU
T10,
RBM
13,C
8orf4
1,RN
F122
,DUS
P26
Biak
aPyg
my
Bantu Eu
rope Mi
deas
tS.
Asia E.
Asia Oc
eania Am
erica
0.05
0.00
1chr1
1 3
4.3
:34.4
AB
TB
2
chr1
0 9
.6:9
.8chr1
9 5
6.8
:56.9
SIG
LE
C5
chr1
9 5
2.2
:52.4
GR
LF
1,N
PA
S1,T
ME
M160,S
AE
1
chr7
106.2
:106.3
PIK
3C
G
chr2
80.1
:80.2
CT
NN
A2
chr1
7 0
.6:0
.8C
17orf
25,R
NM
TL1,N
XN
,GE
MIN
4
chr1
1 2
9.9
:30
KC
NA
4
chr1
3 1
07.7
:107.8
TN
FS
F13B
chr6
164.6
:164.7
chr1
4 8
4.6
:84.7
chr2
0 3
4.9
:35
C20orf
117,C
20orf
118,S
AM
HD
1
chr1
3 2
4.2
:24.3
RN
F17
chr1
9 4
7:4
7.2
LY
PD
4,R
PS
19,A
RH
GE
F1,R
AB
AC
1,A
TP
1A
3,G
RIK
5,D
MR
TC
2,C
EA
CA
M3,C
D79A
chr2
59.1
:59.2
chr1
1 6
3:6
3.2
HR
AS
LS
5,L
GA
LS
12,R
AR
RE
S3,H
RA
SLS
2,H
RA
SLS
3,D
KF
ZP
564J0863
chr1
0 1
2.4
:12.5
CA
MK
1D
chr1
207.1
:207.2
chr2
0 1
6.4
:16.5
C20orf
23
chr1
7 6
0.6
:60.9
RG
S9
chr1
7 5
6.1
:56.4
BC
AS
3
chr1
5 4
6.2
:46.5
SLC
24A
5,M
YE
F2,S
LC
12A
1,D
UT
,FB
N1
chr1
7 5
6.2
:56.7
BC
AS
3
chr8
140:1
40.2
chr5
74.8
:75.1
CO
L4A
3B
P,P
OLK
,C5orf
37
chr1
0 6
5.4
:65.7
chr1
8 1
1.2
:11.3
chr9
90.1
:90.4
SP
IN1,C
9orf
121
chr2
2 4
5:4
5.2
FLJ20699,P
PA
RA
,LO
C150383,P
KD
RE
J,G
TS
E1,T
RM
U,C
ELS
R1
chr1
2 8
7.6
:87.9
chr1
4 6
2.8
:63.1
RH
OJ,G
PH
B5,P
PP
2R
5E
chr1
0 2
2.4
:22.7
CO
MM
D3,B
MI1
,SP
AG
6
chr1
5 4
6.6
:46.8
FB
N1
chr5
26.5
:26.7
chr2
1 1
6.7
:17
C21orf
34
chr1
7 5
0.9
:51.1
chr4
29.5
:29.7
chr3
176.7
:176.9
NA
ALA
DL2
chr7
119.6
:119.9
KC
ND
2
chr2
2 2
1.6
:21.8
RT
DR
1,G
NA
Z
chr1
1 2
5.3
:25.6
chr4
158.7
:159
chr1
5 6
1.6
:61.9
US
P3,F
BX
L22,H
ER
C1
chr2
177.2
:177.5
chr4
41.7
:41.9
SLC
30A
9,C
CD
C4
chr2
17.6
:17.9
VS
NL1,S
MC
6,F
LJ40869
chr2
1 1
6.3
:16.6
C21orf
34
chr6
105.2
:105.5
HA
CE
1
chr5
58.9
:59.2
PD
E4D
chr8
19.5
:19.8
ChG
n,IN
TS
10
chr1
2 6
5.7
:66
CA
ND
1
chr4
95.2
:95.5
SM
AR
CA
D1,P
GD
S
chr8
100.2
:100.5
VP
S13B
chr5
58.6
:58.8
PD
E4D
chr6
105.8
:106
PR
EP
chr1
0 5
9.2
:59.4
chr1
2 1
25.4
:125.6
chr2
177.9
:178.2
AG
PS
,TT
C30A
,TT
C30B
,PD
E11A
chr2
158.4
:158.6
AC
VR
1,U
PP
2
chr2
178.3
:178.6
PD
E11A
chr2
2 4
6.4
:46.7
FLJ46257
chr1
6 1
1.1
:11.4
PR
M1,K
IAA
0350,S
OC
S1,T
NP
2,P
RM
3,P
RM
2,C
16orf
75
chr4
158.2
:158.4
GLR
B,G
RIA
2
Bia
kaP
ygm
y
Bantu E
uro
pe
Mid
east
S.A
sia E.A
sia Oce
ania
Am
erica
0.0
5
0.0
01
Figure 7: Top 10 iHS (A) and XP-EHH (B) signals by population cluster. This isanalogous to Figure 1 in the main text, but uses a window size of 100kb.
10
chr10 106.6:106.8 SORCS3
chr2 81.8:82.2chr11 55:55.6 OR4C15,OR4C11,OR4P4,OR4C6,OR5D13,OR5D14,OR5L1,OR5D18,OR5L2,OR5D16,SPRYD5,OR5W2,OR5I1,OR10AG1,OR5F1,OR5AS1,OR4C16,OR4S2
chr7 117.6:118 ANKRD7,LSM8
chr11 61.2:61.4 C11orf11,C11orf9,C11orf10,FEN1,FADS1,FADS2,FADS3
chr7 106.6:107 HBP1,COG5,DUS4L,GPR22
chr5 75.4:75.6 SV2C
chr11 56:56.2 OR5M8,OR5M11,OR5M10,OR5M1,OR5AP2,OR5AR1
chr10 64.6:65 JMJD1C,REEP3
chr7 127.2:127.4 SND1
chr5 158.4:158.6 EBF1,FLJ31951
chr12 85.8:86.2chr2 50.8:51 NRXN1
chr1 113.6:114 MAGI3
chr20 17.4:17.6 PCSK2,BFSP1,DSTN,RRBP1
chr6 100.8:101 SIM1
chr19 47:47.6 POU2F2,LYPD4,RPS19,ARHGEF1,RABAC1,ATP1A3,GRIK5,ZNF574,DEDD2,ZNF526,GSK3A,ERF,PAFAH1B3,MGC70924,MEGF8,C19orf49,CNFN,LIPE,CIC,TMEM145,DMRTC2,CEACAM3,CD79A
chr14 62.8:63 RHOJ,GPHB5,PPP2R5E
chr13 33:33.4 RFC3
chr15 67.4:67.8 PAQR5,KIF23,RPLP1,LOC729416
chr3 190:190.4 LPP,FAM79B
chr5 11.6:12 CTNND2
chr5 109.6:110.2 SLC25A46
chr6 128.6:129 PTPRK
chr2 21.4:21.8chr18 30.4:30.6 DTNA
chr13 103.6:103.8chr1 35.2:36 SFPQ,ZMYM4,KIAA0319L,NCDN,TFAP2E,PSMB2,FLJ38984,CLSPN,ZMYM1,ZMYM6
chr15 46:46.4 SLC24A5,MYEF2,SLC12A1
chr8 24:24.4 ADAM7,ADAM28,ADAMDEC1
chr12 87.4:88 KITLG
chr5 111.6:111.8 EPB41L4A
chr21 16.6:17 C21orf34
chr3 98.4:98.8 EPHA6
chr9 32.6:32.8 TAF1L,LOC401498
chr17 55.6:56.4 USP32,C17orf64,APPBP2,PPM1D,BCAS3
chr7 119.4:120 KCND2
chr5 117.4:117.8chr4 41.4:42 PHOX2B,TMEM33,WDR21B,SLC30A9,CCDC4
chr2 177.2:177.6chr3 108.6:109.2 BBX
chr15 61.6:62.2 USP3,FBXL22,HERC1,DAPK2,FAM96A,SNX1
chr8 10.8:11.2 C8orf15,MTMR9,XKR6
chr1 103.2:103.6 COL11A1
chr3 25.6:26.2 RARB,TOP2B,NGLY1,OXSM
chr8 138.8:139.2chr8 63.2:64.4 YTHDF3,FAM77D,GGH,TTPA,FLJ39198
chr4 159.2:160 C4orf18,TMEM144,RXFP1,LOC201725,PPID,ETFDH
chr10 44:44.2 CXCL12
chr5 58.8:59.2 PDE4D
chr2 151.6:152 RBM43,NMI,TNFAIP6,RIF1
chr10 110.2:111.2chr4 160.2:160.6
chr9 0.8:1 DMRT1,DMRT3
chr8 9.8:10.2 MSRA
chr4 170.4:171.2 SH3RF1,NEK1,CLCN3,C4orf27,MFAP3L
chr10 59.2:59.6chr2 177.8:178.4 PDE11A,NFE2L2,AGPS,TTC30A,TTC30B
chr1 50.8:51.6 C1orf34,FAF1,CDKN2C,RNF11,EPS15
chr6 122:122.4chr2 158.8:159.4 LOC130940,PKP4,LOC92196
chr3 157.4:157.8 KCNAB1,SSR3
chr6 35.2:35.6 TCP11,SCUBE3,ZNF76,DEF6,FANCE,RPL10A,TEAD3,TULP1,PPARD
chr12 125.4:125.8chr6 49.4:49.8 MUT,CENPQ,C6orf141,RHAG,CRISP2
chr5 155:155.4
BiakaPygmy
BantuEurope
Mideast
S.AsiaE.Asia
Oceania
America
0.05
0.001
Figure 8: Top 10 CLR signals by population cluster. This is analogous to Figure 1 in themain text.
11
Africa−Europe
Cou
nts
040
080
012
00
AB CDEF GHIJ K LMNOP QRS
Africa−E.Asia
Cou
nts
040
080
012
00
A BC DEF GHI J K LMN O PQRS
Europe−E.Asia
Cou
nts
050
010
0015
00
ABCDEFGHIJ KL MNOP QR S
S.Asia−E.AsiaC
ount
s
050
015
00
ABCDEFGHIJ KLMNOP QR S
Africa−S.Asia
FST
Cou
nts
050
010
0015
00
0.0 0.2 0.4 0.6 0.8 1.0
A BCDEF GHI J KLMNOP QRS
Europe−S.Asia
FST
Cou
nts
050
015
00
0.0 0.2 0.4 0.6 0.8 1.0
AB CDEFGHIJKLMNOP QRS
Fst
Cou
nts
ABCDEFGHIJ
CETPLPLLIPCABCA1LIPGAPOC_clustAPOBLDLRAPOA_clustGCKR
KLMNOPQRS
LPL_2
SORT1PDSK9GALNT2MVKNCANTRIB1MLXIPLANGPTL3
Figure 9: FST surrounding loci involved in natural variation in lipid levels. This figurewas generated as in Figures 3 and 4 in the main text.
12
Africa−Europe
Cou
nts
040
080
012
00
A BCD E FG HI JKL MNOP QRST UVWXY Z1 234
Africa−E.Asia
Cou
nts
040
080
012
00
ABCD EF GHIJK LM NOPQRS TUVW XYZ 12 34Europe−E.Asia
Cou
nts
050
010
0015
00
AB CDEFGHI JK LM NOPQRS TUVWXY Z123 4
S.Asia−E.AsiaC
ount
s
050
015
00
AB CDE F GHI JK LM NOP QRS TUVWXYZ12 3 4
Africa−S.Asia
FST
Cou
nts
050
010
0015
00
0.0 0.2 0.4 0.6 0.8 1.0
ABCD EFG HI JKLMN OP QRSTUVWXY Z1 234
Europe−S.Asia
FST
Cou
nts
050
015
00
0.0 0.2 0.4 0.6 0.8 1.0
ABCD EFGHI JKLMNOPQRSTUVWXYZ1234
Fst
Cou
nts
ABCDEFGHIJ
IL23RATG16L1MST1PTGER45q31IRGMTNFSF15ZNF365NKX2−3NOD2
KLMNOPQRST
PTPN2PTPN22ITLN11q241q32IL12BCDKAL16q21CCR67p12
UVWXYZ1234
8q24JAK210p11C11orf30LRKK213q14ORMDL3STAT321q21ICOSLG
Figure 10: FST surrounding loci involved in natural variation in susceptibility to Crohn’sdisease. This figure was generated as in Figures 3 and 4 in the main text.
13
Africa−Europe
FST
Cou
nts
040
080
012
00
ABC D EF GHI J KLMNO PQR ST UVWXYZ1 2345678 9 abcdef gh
Africa−E.Asia
Cou
nts
040
080
012
00
AB CDE FGHI J KLMNOPQ R ST UVW X YZ1 23 456 789 abcd efg h
Europe−E.Asia
Cou
nts
050
010
0015
00
ABCDE FGHI JKLMNO PQRSTU VWXYZ12 3 45 67 8 9a bcd efgh
S.Asia−E.AsiaC
ount
s
050
015
00
A BCDE FGHI JKLM NOPQR STU VWXYZ12 345 678 9a bcd efghAfrica−S.Asia
FST
Cou
nts
050
010
0015
00
0.0 0.2 0.4 0.6 0.8 1.0
ABCD EFG HI J KLMNOP QR ST UVWXYZ1 2345 6789 abcdefgh
Europe−S.Asia
FST
Cou
nts
050
015
00
0.0 0.2 0.4 0.6 0.8 1.0
ABCDEFGHIJK LMNO PQRSTUVWXYZ 123456789abcdef gh
Fst
Cou
nts
ABCDEFGHIJKLMNO
ZBTB38CDK6HMGA2GDF5LCORLLOC387103EFEMP1C6orf106PTCH1SPAG17SOCS2HHIPZNF678DLEU7SCMH1
PQRSTUVWXYZ1234
ADAMTSL3IHHCEP63ACANDYM1q12DNM3C1orf19BMP66p22BAT3TNXB6p21EGPR126GNA12
5
6
7
8
9a
bc
de
fg
h
PLAG18q21
ZNF46214q32
ADAMTS1717q11
17q23A
17q23B
18q11
BMP2
LIN28B
DOTL1
CDCHD7
Figure 11: FST surrounding loci involved in natural variation in height. This figure wasgenerated as in Figures 3 and 4 in the main text.
14
Pygmy−Bantu
FST
Cou
nts
050
010
0015
0020
0025
00
0.0 0.2 0.4 0.6 0.8 1.0
ABC D
EFG H
I JK
LM
NO
PQ RS TU VWX
YZ12
345 67
89abc
d
ef
gh
A
B
C
D
E
F
G
H
I
J
K
L
M
N
O
ZBTB38
CDK6
HMGA2
GDF5
LCORL
LOC387103
EFEMP1
C6orf106
PTCH1
SPAG17
SOCS2
HHIP
ZNF678
DLEU7
SCMH1
P
Q
R
S
T
U
V
W
X
Y
Z
1
2
3
4
ADAMTSL3
IHH
CEP63
ACAN
DYM
1q12
DNM3
C1orf19
BMP6
6p22
BAT3
TNXB
6p21E
GPR126
GNA12
5
6
7
8
9
a
b
c
d
e
f
g
h
PLAG1
8q21
ZNF462
14q32
ADAMTS17
17q11
17q23A
17q23B
18q11
BMP2
LIN28B
DOTL1
CDCHD7
Figure 12: FST between Bantu and Pygmy populations surrounding loci involved innatural variation in height. This figure was generated as in Figures 3 and 4 in the main text.
15
chr19 43.4:43.6 RYR1,SIPA1L3,DPF1,PPP1R14A,SPINT2,LOC541469,C19orf33,YIF1B,KCNK6,C19orf15,PSMD8,GGN,SPRED3,RASGRP4,FAM98C
chr9 11.8:12chr11 109.8:110.2 FDX1,ARHGAP20
chr14 97.6:97.8chr13 87.8:88
chr10 20.4:20.6 PLXDC2
chr11 9.8:10.2 SBF2
chr9 99.6:99.8 ANP32B,C9orf156,FOXE1,HEMGN
chr16 22.8:23 HS3ST2,USP31
chr4 119.8:120 KIAA1627,SEC24D,SYNPO2
chr4 119.2:119.6 NDST3,PRSS12
chr5 109:109.2 MAN2A1
chr3 4.4:4.6 SUMF1,ITPR1
chr1 200.8:201 PPP1R12B,SYT2,JARID1B
chr19 56.6:56.8 ETFB,CLDND2,NKG7,LIM2,SIGLEC12,SIGLEC6,ZNF175,SIGLEC5,SIGLEC10,SIGLEC8,LOC729767
chr2 155.4:155.6 KCNJ3
chr8 49.2:49.4chr8 140.2:140.4
chr20 46.6:47 PREX1,ARFGEF2
chr3 165.4:165.6chr12 78:78.2 SYT1
chr22 34.2:34.4 MCM5,RASD2,MB,LOC284912,APOL6,APOL5
chr6 100.8:101 SIM1
chr3 165:165.2chr9 114:114.2 SUSD1,ROD1,HSDL2
chr16 80:80.2 GAN,CMIP
chr2 12.2:12.4chr12 81.4:81.6 C12orf26,TMTC2
chr17 3.4:3.6 TRPV1,CTNS,TRPV3,CARKL,TAX1BP3,TMEM93,P2RX5,ITGAE,GSG2
chr7 20.4:20.6 ITGB8
chr13 29.4:29.6 LOC440131
chr12 28:28.2 PTHLH
chr4 163:163.2 FSTL5
chr11 112.4:112.6 NCAM1
chr7 156.2:156.4 RNF32,LMBR1,NOM1
chr9 28.6:28.8 LINGO2
chr18 40.8:41.2 SETBP1
chr14 31.2:31.4 NUBPL
chr9 138.8:139 MAMDC4,LCN10,LCN6,LCN8,UNQ2541,TMEM141,C9orf86,PHPT1,EDF1,TRAF2,FBXW5,C8G,PTGDS,FLJ45224,C9orf142,CLIC3,ABCA2,C9orf139,FUT7,KIAA1984,LCN12,LOC389813
chr8 21.2:21.4chr11 6:6.2 OR52L1,OR56A1,OR56B4,OR52B2,OR52W1,C11orf42,C11orf56,CNGA4,CCKBR,OR56A4
chr8 113.8:114 CSMD3
chr9 94.6:94.8 ANKRD19,BICD2,ZNF484,FGD3
chrX 137.8:138chr6 130.6:130.8 SAMD3,KIAA1913
chr3 100.8:101 COL8A1,FLJ44076,C3orf26,FILIP1L
chr4 139:139.2chr9 24:24.2
chr18 42.2:42.4 RNF165,LOXHD1
chr6 72.8:73 RIMS1
chr9 110.8:111 EPB41L4B,C9orf4,C9orf5,CTNNAL1
chr13 57:57.2 PCDH17
chr13 56.4:56.6 FLJ40296
chr9 114.6:114.8 TSCOT,ZFP37
chr3 56.6:56.8 CCDC66,C3orf63,ARHGEF3
chr18 64.8:65 CCDC102B
chr11 83.8:84 DLG2
chr22 34.8:35 APOL3,APOL4,APOL2,APOL1,MYH9
chr4 34.2:34.4chr6 77:77.2
chr11 87.4:87.6 RAB38
chr3 118.4:118.6chr5 66.8:67.2
chr3 46:46.2 FYCO1,CXCR6,XCR1,CCR1
chr12 80.6:80.8 PPFIA2
chr16 25.8:26 HS3ST4
chr11 40.4:40.6chr3 61:61.2 FHIT
chr6 26.4:26.6 HIST1H4G,HIST1H3F,HIST1H2BH,HIST1H3G,HIST1H2BI,HIST1H4H,BTN3A2,BTN2A2,BTN3A1,BTN2A3,BTN3A3,BTN2A1,BTN1A1,HMGN4
chr1 79.6:79.8chr5 43:43.2 AXIIR,ZNF131,MGC42105
chr21 29.4:29.6 CCT8,C21orf7,BACH1
chr6 29.6:29.8 MAS1L,OR2H2,GABBR1,MOG,HLA−F
chr2 98.2:98.4 INPP4A,MGC26733,CNGA3
chr7 92:92.2 MGC40405,CDK6,DKFZP564O0523,PEX1
chr15 54.2:54.4 RFXDC2,TEX9
chr1 79:79.2chr7 82.6:82.8 SEMA3E
chr7 141:141.2 AGK,FLJ40852,SSBP1,TAS2R3,TAS2R4,TAS2R5,LOC136242,KIAA1147
chr14 71.8:72 RGS6
chr1 173.4:173.6 TNN,KIAA0040,TNR
chr8 5.2:5.4chr4 130.2:130.4 SCLT1,C4orf33
chr3 76.8:77chr1 88.8:89 PKN2
chr5 162:162.2chr9 76:76.2chr8 9.2:9.4
chr21 43:43.2 PDE9A,WDR4,NDUFV3
chrX 125:125.2 WDR40C
chr10 90.2:90.4 C10orf59,LIPL1,LIPF
chr8 68.8:69 CPA6,DEPDC2
chr6 70.6:70.8 LMBRD1,COL19A1
chr9 81:81.2chr6 75.4:75.6
chr5 145.8:146 TCERG1,GPR151,PPP2R2B
chr5 163.4:163.6chr17 42.6:42.8 CDC27,MYL4,ITGB3,C17orf57
chr15 59.8:60 VPS13C
chr21 44.8:45 C21orf29,KRTAP10−1,KRTAP10−2,KRTAP10−3,KRTAP10−4,KRTAP10−5,KRTAP10−6,KRTAP10−7,KRTAP10−8,KRTAP10−9,KRTAP10−10,KRTAP10−11,KRTAP12−4,KRTAP12−3,KRTAP12−2,KRTAP12−1,KRTAP10−12,UBE2G2,SUMO3
chr10 58:58.2chr12 5.2:5.4
chr2 86.6:86.8 JMJD1A,VPS24,RNF103,RMND5A
chr10 68.8:69 CTNNA3
chr15 74.4:74.6 ISL2,ZNF291,ETFA
BiakaPygmy
BantuEurope
Mideast
S.AsiaE.Asia
Oceania
America
0.05
0.001
Figure 13: The top 1% of iHS signals in the Bantu, ordered from top to bottom in order ofsignificance. See the caption of Figure 1 in the main text for details.
16
chr9 31.2:31.6chr7 66.6:67
chr2 97.6:97.8 COX5B,ACTR1B,ZAP70,KIAA1641
chr5 109:109.2 MAN2A1
chr6 26.4:26.6 HIST1H4G,HIST1H3F,HIST1H2BH,HIST1H3G,HIST1H2BI,HIST1H4H,BTN3A2,BTN2A2,BTN3A1,BTN2A3,BTN3A3,BTN2A1,BTN1A1,HMGN4
chr3 29.4:29.8 RBMS3
chr11 57.8:58 OR10Q1,OR10W1,OR5B17,OR5B3,OR5B2,OR5B12,OR5B21
chr3 133.2:133.4 CPNE4
chr6 85.4:85.6 TBX18
chr13 35.4:35.6 DCAMKL1,SOHLH2
chr2 99.6:99.8 AFF3
chr9 86:86.2 SLC28A3
chr9 75.2:75.4chr15 53.8:54 PRTG,NEDD4
chr3 75:75.2chr15 54.8:55 SUHW4,TCF12
chr9 13.6:13.8chr12 70.6:70.8 TBC1D15,TPH2
chr15 55.2:55.4 TCF12
chr2 55:55.2 RTN4,FLJ42562
chr4 160.8:161.2chr5 130:130.2
chr3 155.2:155.4 SGEF
chr1 5:5.2chr16 11:11.2 KIAA0350
chr2 173:173.2 ITGA6,PDK1
chr7 28.6:28.8 CREB5
chr19 36.6:36.8chr10 19:19.2 NSUN6,ARL5B
chr3 27.2:27.4 NEK10,SLC4A7
chr7 29.8:30 SCRN1,FKBP14,PLEKHA8,WIPF3
chr7 40.6:40.8 C7orf10
chr5 123:123.2 CSNK1G3
chr18 40.8:41 SETBP1
chr20 57.6:57.8 PHACTR3
chr2 43.6:43.8 THADA,PLEKHH2
chr10 67.4:67.6 CTNNA3
chr2 84.6:84.8 FLJ37357
chr7 84.2:84.4chr11 16.4:16.6 SOX6
chr11 76.6:76.8 GDPD4,PAK1,MYO7A
chr18 19.2:19.4 RIOK3,C18orf8,NPC1,ANKRD29,C18orf45
chr3 20:20.2 C3orf48,EFHB,RAB5A,PCAF,SGOL1
chr10 3:3.2 PFKP,PITRM1
chr1 189.8:190chr13 57.4:57.6chr5 14.2:14.4 TRIO
chr7 9.4:9.6chr5 26.6:26.8chr2 42.2:42.4 EML4,COX7A2L
chr2 229.8:230 DNER,PID1
chr5 136.2:136.4 SPOCK1
chr2 46.4:46.6 EPAS1,ATP6V1E2,RHOQ
chr2 84.2:84.4 LOC388965
chr2 98.2:98.4 INPP4A,MGC26733,CNGA3
chr6 23.8:24chr6 115.8:116
chr6 154.2:154.4 OPRM1
chr7 125.4:125.6chr11 73.6:73.8 DKFZP586P0123,PPME1,P4HA3,PGM2L1,KCNE3
chr15 42.8:43 B2M,TRIM69,C15orf43
chr2 50.2:50.4 NRXN1
chr15 51.2:51.4chr6 159.8:160.2 SOD2,WTAP,ACAT2,TCP1,MRPL18,PNLDC1,MAS1
chr6 19:19.2chr7 2.8:3 GNA12,CARD11
chr15 97.4:97.6 TTC23,LRRC28,DMN
chr2 209.8:210 MAP2
chr5 140.8:141 PCDHGA1,PCDHGA2,PCDHGA3,PCDHGB1,PCDHGA4,PCDHGB2,PCDHGA5,PCDHGB3,PCDHGA6,PCDHGA7,PCDHGB4,PCDHGA8,PCDHGB5,PCDHGA9,PCDHGB6,PCDHGA10,PCDHGB7,PCDHGA11,PCDHGA12,PCDHGC3,PCDHGC4,PCDHGC5,HDAC3,C5orf16,FCHSD1,CENTD3,DIAPH1
chr15 63.2:63.4 PDCD7,CLPX,CILP,PARP16,PUNC
chr3 76.8:77chr3 3.6:3.8 LRRN1
chr5 108.4:108.6 FER
chr6 131.2:131.4 EPB41L2
chr5 18.2:18.4chr13 90.4:90.6
chr3 63:63.2chr20 37.8:38
chr5 135.4:135.6 TGFBI,SMAD5,TRPC7
chr14 64.8:65 FUT8
chr14 80.4:80.6 C14orf145,TSHR
chr9 114.6:114.8 TSCOT,ZFP37
chrX 145.6:145.8chr2 25.2:25.4 POMC,DNMT3A
chr22 31.6:31.8 SYN3,TIMP3
chr8 69.6:69.8 C8orf34
chr1 5.8:6 NPHP4,KCNAB2
chr11 38.4:38.6chr11 104.6:104.8
chr1 79:79.2chr21 40.8:41 DSCAM
chr9 110.8:111 EPB41L4B,C9orf4,C9orf5,CTNNAL1
chr4 130.2:130.4 SCLT1,C4orf33
chr5 160.2:160.4chr16 78.6:78.8
chr5 129.2:129.4 CSS3
chr6 56:56.2 COL21A1
chr18 60.2:60.4chr6 2.2:2.4 GMDS
chr6 133:133.2 TAAR2,TAAR5,TAAR1,VNN1,VNN3,VNN2,C6orf192,RPS12
chr10 119.4:119.6
BiakaPygmy
BantuEurope
Mideast
S.AsiaE.Asia
Oceania
America
0.05
0.001
Figure 14: The top 1% of iHS signals in the Biaka Pygmies, ordered from top to bottom in orderof significance. See the caption of Figure 1 in the main text for details.
17
chr2 167.6:168 CMYA3
chr17 60.6:60.8 RGS9
chr9 107:107.2 SLC44A1
chr14 60.8:61.2 TMEM30B,PRKCH,HIF1A
chr5 112.4:112.6 DCP2,MCC
chr4 60.6:61chr9 3.2:3.4 RFX3
chr3 131.4:131.8 FLJ35880
chr3 25.8:26 NGLY1,OXSM
chr2 178:178.2 PDE11A,AGPS,TTC30A,TTC30B
chr8 52.6:53 PCMTD1
chr8 139.6:139.8 C8ORFK32,COL22A1
chr7 119.8:120.2 KCND2,TSPAN12
chr6 30:30.4 HLA−A,HCG9,ZNRD1,RNF39,TRIM31,TRIM40,TRIM15,TRIM26,FLJ45422,TRIM39,RPP21,PPP1R11
chr18 19.6:19.8 LAMA3,C18orf17
chr2 197.4:197.6 GTF3C3,UNQ6411,PGAP1,ANKRD44
chr5 145.8:146.2 TCERG1,GPR151,PPP2R2B
chr8 140:140.2 COL22A1
chr15 91.8:92chr5 21.8:22 CDH12
chr2 158.2:158.6 ACVR1C,ACVR1,UPP2
chr2 195.4:195.6chr15 67.2:67.4 GLCE,PAQR5
chr6 105.8:106 PREP
chr9 12.4:12.8 TYRP1,C9orf150
chr4 34:34.2chr10 83.6:83.8 NRG3
chr5 74.6:74.8 HMGCR,COL4A3BP,POLK
chr16 80.8:81 MPHOSPH6
chr4 186.4:186.6 SNX25,LRP2BP,ANKRD37,C4orf20,CCDC110
chr14 62.8:63 RHOJ,GPHB5,PPP2R5E
chr9 125.4:125.6 DENND1A
chr5 142:142.4 FGF1,ARHGAP26
chr12 40:40.2 PDZRN4
chr7 36.8:37.2 ELMO1
chr4 148.4:148.6 EDNRA
chr1 65.2:65.4 AK3L1,AK3L2,JAK1
chr18 7.4:7.6 PTPRM
chr1 160.2:160.6 ATF6,OLFML2B,NOS1AP,C1orf111,SH2D1B
chr21 29.8:30 GRIK1
chr4 32.6:32.8chr12 101:101.2 CCDC53,NUP37,PMCH,C12orf48
chr2 238:238.2 COL6A3,PRLH,RAB17,MLPH
chr10 84:84.2 NRG3
chr12 110.2:110.4 FAM109A,SH2B3,ATXN2,CUTL2
chr1 244:244.2 SMYD3
chr5 23.2:23.4chr18 24.8:25
chr6 24.2:24.4 NRSN1,DCDC2
chr8 30:30.2 TMEM66,LEPROTL1,DCTN6
chr9 86.4:86.6 NTRK2
chr10 115:115.2chr7 19.2:19.4 FERD3L
chr4 29.8:30chr17 51.2:51.4 TMEM100,PCTP
chr16 78.2:78.6 MAF
chr9 93.2:93.4 AUH,NFIL3
chr2 40.2:40.4 SLC8A1
chr15 85.2:85.4 AGBL1
chr1 11.4:11.6 FBXO2,FBXO44,FBXO6
chr9 110.8:111 EPB41L4B,C9orf4,C9orf5,CTNNAL1
chr15 27:27.2 APBA2
chr11 20.8:21 NELL1
chr2 123:123.2chr5 24.6:24.8 CDH10
chr14 63.4:63.6 SYNE2
chrX 24:24.2 KLHL15,EIF2S3,ZFX
chrX 93.2:93.4chr6 30.6:30.8 IER3,PRR3,HLA−E,GNL1,ABCF1,PPP1R10,MRPS18B,C6orf134,C6orf136,DHX16,NRM,MDC1,TUBB,FLOT1
chr4 41.2:41.6 DKFZP686A01247,PHOX2B,TMEM33
chr3 72.6:72.8 RYBP
chr3 100.6:100.8 COL8A1
chr13 18.6:18.8 TUBA3C
chr4 14.2:14.4chr5 38:38.2
chr12 61:61.2 USP15,MON2
chr17 9.4:9.6 WDR16,STX8,USP43
chr9 130:130.2 LCN2,CIZ1,DNM1,GOLGA2,TRUB2,COQ4,SLC27A4,URM1,CEECAM1,C9orf16
chr12 11.4:11.6 PRB4,PRB1,PRB2
chr11 87.2:87.4chr12 123.2:123.4 NCOR2,FAM101A
chr7 7.2:7.4 C1GALT1,COL28A1
chr16 76.8:77 WWOX
chr2 147.4:147.6chr8 52:52.2
chr16 1.6:1.8 MAPK8IP3,IFT140,CRAMP1L,HN1L,NME3,MRPS34,EME2,SPSB3,NUBP2,IGFALS,FAHD1,C16orf73,HAGH
chr22 30.2:30.4 DRG1,EIF4ENIF1,SFI1,PISD,C22orf30
chr6 102.2:102.4 GRIK2
chr6 167.2:167.4 RPS6KA2,RNASET2,FGFR1OP
chr5 115.6:115.8 COMMD10,SEMA6A
chr3 103.6:103.8 ZPLD1
chr17 74.4:74.6 TIMP2,LGALS3BP,CANT1,C1QTNF1,FLJ21865
chr2 196.6:196.8 DNAH7,STK17B,HECW2
BiakaPygmy
BantuEurope
Mideast
S.AsiaE.Asia
Oceania
America
0.05
0.001
Figure 15: The top 1% of iHS signals in the Europeans, ordered from top to bottom in order ofsignificance. See the caption of Figure 1 in the main text for details.
18
chr9 107:107.2 SLC44A1
chr2 212.8:213.2 ERBB4
chr4 34:34.2chr14 62.6:63 KCNH5,RHOJ,GPHB5,PPP2R5E
chr5 19.6:20 CDH18
chr8 139.6:139.8 C8ORFK32,COL22A1
chr17 60.6:60.8 RGS9
chr15 27:27.2 APBA2
chr7 119.8:120.2 KCND2,TSPAN12
chr3 25.8:26 NGLY1,OXSM
chr18 64.8:65 CCDC102B
chr10 84:84.4 NRG3
chr20 21.2:21.4 C20orf19,XRN2,NKX2−2
chr12 40:40.4 PDZRN4
chr9 125.2:125.6 CRB2,DENND1A
chr14 61:61.2 PRKCH,HIF1A
chr21 29.6:30 BACH1,GRIK1
chr22 45:45.2 FLJ20699,PPARA,LOC150383,PKDREJ,GTSE1,TRMU,CELSR1
chr1 244:244.2 SMYD3
chr1 65:65.2 RAVER2,JAK1
chr2 238:238.2 COL6A3,PRLH,RAB17,MLPH
chr8 116.8:117 TRPS1
chr8 140:140.2 COL22A1
chr12 124.6:124.8 TMEM132B
chr5 145.8:146 TCERG1,GPR151,PPP2R2B
chr5 30.6:30.8chr11 129.4:129.6 PRDM10,C11orf37,APLP2,ST14,ZBTB44
chr6 108:108.2 SCML4,FLJ10159
chr2 158.2:158.6 ACVR1C,ACVR1,UPP2
chr4 60.6:61chr5 142:142.4 FGF1,ARHGAP26
chr10 22.4:22.6 COMMD3
chr3 131.6:131.8 FLJ35880
chr5 110.2:110.4 TSLP
chr3 113:113.2 TMPRSS7,PLCXD2,PHLDB2,ABHD10,TAGLN3
chr12 125.6:125.8chr2 72.2:72.4 CYP26B1
chr7 33.6:33.8 BBS9
chr15 67.4:67.6 GLCE,PAQR5,KIF23,RPLP1,LOC729416
chr16 1.6:1.8 MAPK8IP3,IFT140,CRAMP1L,HN1L,NME3,MRPS34,EME2,SPSB3,NUBP2,IGFALS,FAHD1,C16orf73,HAGH
chr16 77:77.2 WWOX
chr12 98.2:98.4 ANKS1B
chr12 10:10.4 FLJ46363,CLEC12A,CLEC1B,CLEC12B,CLEC9A,CLEC1A,CLEC7A,GABARAPL1,KLRD1,KLRK1,C12orf59,OLR1
chr2 195.4:195.6chrX 19:19.2 GPR64
chr22 48.6:48.8 MLC1,BRD1,ZBED4,ALG12,CRELD2,PIM3,FLJ41993,LOC164714
chr20 22.2:22.6 FOXA2
chr17 59.6:59.8 ERN1,TEX2,PECAM1
chr3 64.2:64.4 PRICKLE2
chr14 63.4:63.6 SYNE2
chr12 87.2:87.4 KITLG
chr20 48.8:49 PARD6B,BCAS4,ADNP,DPM1,MOCS3
chr8 52.8:53 PCMTD1
chr4 170.2:170.6 CBR4,SH3RF1,NEK1
chr11 83.4:83.6 DLG2
chr13 73.8:74chr4 29.8:30
chr14 23.8:24 C14orf124,TGM1,CHMP4A,MDP−1,NEDD8,GMPR2,TINF2,RABGGTA,DHRS1,C14orf21,LTB4R2,LTB4R,ADCY4,NFATC4,KIAA0323,CMA1,RIPK3,CIDEB,CBLN3
chr2 1.8:2 MYT1L
chr17 51:51.2 TMEM100,PCTP
chr1 212.4:212.6 SMYD2,PTPN14
chr10 83.6:83.8 NRG3
chr15 91.8:92chr1 246.2:246.4 OR2T8,OR2L13,OR2L8,OR2AK2,OR2L2,OR2L3,OR2M5,OR2M2,OR2M3
chr2 21.6:21.8chr8 116:116.2
chr13 103:103.2chr5 21.8:22 CDH12
chr4 148.4:148.6 EDNRA
chr7 124.2:124.4 POT1,GPR37,LOC401398
chr8 55.2:55.4 LYPLA1,MRPL15
chr20 52.6:52.8 DOK5
chr11 17.6:17.8 MYOD1,SERGEF,KCNC1
chr4 43:43.2chr5 92.4:92.6
chr2 152.2:152.4 NEB,ARL5A,CACNB4
chr5 24.6:24.8 CDH10
chr6 30:30.4 HLA−A,HCG9,ZNRD1,RNF39,TRIM31,TRIM40,TRIM15,TRIM26,FLJ45422,TRIM39,RPP21,PPP1R11
chr12 110.2:110.4 FAM109A,SH2B3,ATXN2,CUTL2
chr4 14.2:14.4chr17 72.2:72.4 ST6GALNAC1,MXRA7,SFRS2,MFSD11,MGAT5B,PTDSR,LOC124512
chr4 5.2:5.4 STK32B
chr5 115.6:115.8 COMMD10,SEMA6A
chr20 54:54.2 CBLN4
chr12 65.8:66 CAND1
chrX 33.8:34chr6 54.8:55 FAM83B
chr3 88:88.2 HTR1F,CGGBP1
chr8 84.6:84.8chr7 125.8:126 GRM8
chr4 130:130.2 PHF17,SCLT1,C4orf33
chr5 112.4:112.6 DCP2,MCC
chr15 64.8:65 SMAD6
chr18 7.4:7.6 PTPRM
chr5 74.6:74.8 HMGCR,COL4A3BP,POLK
chr8 42.6:42.8 CHRNA6,THAP1,RNF170,CHRNB3
chr15 46:46.2 SLC24A5,MYEF2
BiakaPygmy
BantuEurope
Mideast
S.AsiaE.Asia
Oceania
America
0.05
0.001
Figure 16: The top 1% of iHS signals in the Middle East, ordered from top to bottom in order ofsignificance. See the caption of Figure 1 in the main text for details.
19
chr15 46:46.4 SLC24A5,MYEF2,SLC12A1,DUT
chr17 51:51.4 TMEM100,PCTP
chr7 119.8:120.2 KCND2,TSPAN12
chr14 62.6:63 KCNH5,RHOJ,GPHB5,PPP2R5E
chr8 11:11.2 C8orf15,MTMR9,AMAC1L2,XKR6
chr22 45:45.2 FLJ20699,PPARA,LOC150383,PKDREJ,GTSE1,TRMU,CELSR1
chr10 83.8:84.2 NRG3
chr3 25.8:26 NGLY1,OXSM
chr6 73.8:74 C6orf148,KCNQ5
chr8 139.6:139.8 C8ORFK32,COL22A1
chr9 125.2:125.6 CRB2,DENND1A
chr6 30.2:30.6 PRR3,RNF39,TRIM31,TRIM40,TRIM15,TRIM26,FLJ45422,TRIM39,RPP21,HLA−E,GNL1,ABCF1
chr9 122.6:123 FBXW2,PSMD5,PHF19,TRAF1,C5,CEP110,RAB14
chr3 131.6:131.8 FLJ35880
chr2 237.2:237.4 CXCR7
chr1 234.8:235 LGALS8,HEATR1,ACTN2,MTR
chr9 107:107.2 SLC44A1
chr21 29:29.2 N6AMT1,ZNF294
chr4 34:34.4chr20 15.6:15.8 C20orf133
chr2 158.2:158.6 ACVR1C,ACVR1,UPP2
chr2 231.4:231.6 GPR55,CAB39,ITM2C,PSMD1
chr9 130:130.2 LCN2,CIZ1,DNM1,GOLGA2,TRUB2,COQ4,SLC27A4,URM1,CEECAM1,C9orf16
chr6 105.6:106 LIN28B,BVES,POPDC3,PREP
chr4 29.6:30chr5 117.4:117.6
chr15 27:27.2 APBA2
chr5 145.8:146 TCERG1,GPR151,PPP2R2B
chr17 60.6:60.8 RGS9
chr3 142.2:142.4 SLC25A36,SPSB4,ACPL2
chr4 41.4:41.6 DKFZP686A01247,PHOX2B,TMEM33
chr18 64.8:65 CCDC102B
chr5 112.4:112.6 DCP2,MCC
chr2 218.8:219 GPBAR1,PNKD,ARPC2,TMBIM1,MGC50811,SLC11A1,CTDSP1,VIL1,USP37,AAMP
chr12 81.8:82 TMTC2
chr8 21.8:22 NUDT18,DOK2,XPO7,NPM2,FGF17,EPB49,RAI16,HR
chr21 16.2:16.4 USP25,C21orf34
chr7 86.4:86.6 KIAA1324L,DMTF1
chr3 25.4:25.6 RARB,TOP2B
chr16 78.4:78.6chr2 223.4:223.8 ACSL3,KCNE4
chr12 98.2:98.4 ANKS1B
chrX 66.4:66.6chr14 64.2:64.6 PLEKHG3,SPTB,CHURC1,GPX2,RAB15,FNTB,MAX
chr2 178:178.2 PDE11A,AGPS,TTC30A,TTC30B
chr5 25:25.2chr9 86.4:86.6 NTRK2
chr13 67:67.2chr8 52.6:53 PCMTD1
chr3 66.8:67chr8 92:92.2 EFCBP1,TMEM55A,OTUD6B
chr11 129.4:129.6 PRDM10,C11orf37,APLP2,ST14,ZBTB44
chr9 93.6:93.8 ROR2,SPTLC1
chr20 48.8:49 PARD6B,BCAS4,ADNP,DPM1,MOCS3
chr8 10.6:10.8 RP1L1,C8orf74,SOX7,PINX1,XKR6
chr8 42.6:42.8 CHRNA6,THAP1,RNF170,CHRNB3
chr10 59.4:59.8 IPMK,ZCD1,UBE2D1,TFAM
chr21 29.4:29.8 CCT8,C21orf7,BACH1,GRIK1
chr7 37:37.2 ELMO1
chr11 113.4:113.6 HTR3A,ZBTB16
chr22 33.6:33.8 ISX
chr5 38:38.2chr12 79.2:79.4 C12orf64
chr4 180.2:180.4chr13 103:103.2chr4 173.8:174 GALNT17
chr4 170.2:170.4 CBR4,SH3RF1
chr14 63.4:63.6 SYNE2
chr15 64.8:65 SMAD6
chr13 74:74.2chr9 32.6:32.8 NDUFB6,TAF1L,LOC401498
chr2 196.6:196.8 DNAH7,STK17B,HECW2
chr20 9.4:9.6 PLCB4,C20orf103,PAK7
chr12 18.8:19 PLCZ1,CAPZA3
chr8 140:140.2 COL22A1
chr20 22.4:22.6 FOXA2
chr8 98.4:98.6 TSPYL5
chr12 92.4:92.6 UBE2N,MRPL42,SOCS2,CRADD
chr6 29.2:29.4 OR2B3,OR5U1,OR5V1,OR12D3,LOC651503
chr7 148.4:148.6 ZNF783,PDIA4,ZNF786,ZNF425,ZNF398,ZNF212,ZNF282
chr12 87.2:87.4 KITLG
chr16 82.4:82.6 CDH13,HSBP1,EFCBP2,MBTPS1,OSGIN1,MLYCD,LOC146167
chr6 83.4:83.6chr22 24.2:24.4 ADRBK2
chr7 118.2:118.4chrX 121.2:121.4chr3 176.6:176.8 NAALADL2
chr11 87.2:87.4chr5 121:121.2 FTMT
chr13 59:59.2 DIAPH3
BiakaPygmy
BantuEurope
Mideast
S.AsiaE.Asia
Oceania
America
0.05
0.001
Figure 17: The top 1% of iHS signals in South Asia, ordered from top to bottom in order ofsignificance. See the caption of Figure 1 in the main text for details.
20
chr2 108.8:109 RANBP2,FLJ32745,EDAR
chr2 212.6:213 ERBB4
chr6 125.8:126.2 HEY2,NCOA7
chr2 108:108.4 SLC5A7,SULT1C3,SULT1C1,SULT1C2,GCC2
chr10 55.6:55.8 PCDH15
chr10 94.8:95.2 EXOC6,CYP26C1,CYP26A1,FER1L3,CEP55
chr5 112.2:112.6 APC,SRP19,DCP2,MCC,REEP5
chr10 55:55.2
chr11 25.2:25.6
chr12 1.2:1.4 ERC1
chr13 103.8:104
chr2 125.8:126.2
chr17 45.8:46.2 MRPL27,EME1,LRRC59,FLJ20920,CHAD,RSAD1,EPN3,SPATA20,CACNA1G,ABCC3,ANKRD40,CROP,XYLT2,MYCBPAP
chr4 170.2:170.6 CBR4,SH3RF1,NEK1
chr9 110.2:110.6
chr13 62.6:62.8
chr8 32:32.2 NRG1
chr22 38.2:38.4 MAP3K7IP1,MGAT3,SMCR7L,ATF4,RPS19BP1,CACNA1I
chr2 17:17.4
chr1 73.6:73.8
chr5 108:108.2 FER
chr5 25:25.2
chr10 52.8:53 PRKG1
chr10 94.4:94.6 KIF11,HHEX,EXOC6
chr20 58.2:58.4 LOC284757
chr9 125.2:125.6 CRB2,DENND1A
chr16 17.2:17.4 XYLT1
chr7 86.2:86.4 GRM3,KIAA1324L
chr2 172.8:173.2 ITGA6,PDK1
chr16 64.2:64.4
chr2 38.2:38.4 CYP1B1,MGC34824,ARL6IP2
chr1 65.8:66 LEPR,PDE4B
chr4 105.2:105.6 CXXC4
chr15 62:62.2 DAPK2,FAM96A,SNX1,SNX22,PPIB,CSNK1G1
chr7 3.8:4.2 SDK1
chr10 11:11.2 CUGBP2
chr16 76:76.2 ADAMTS18
chr1 75.6:76 SLC44A5,ACADM,RABGGTB,MSH4
chr4 158.6:159
chr9 110.8:111 EPB41L4B,C9orf4,C9orf5,CTNNAL1
chr1 103.2:103.4 COL11A1
chr4 28.2:28.6
chr6 159:159.2 DYNLT1,VIL2,LOC202459,SYTL3
chr3 71.4:71.6 FOXP1
chr2 29.2:29.4 FLJ34931,CLIP4,ALK
chr10 4.2:4.4
chr22 34.8:35.2 APOL3,APOL4,APOL2,APOL1,MYH9,TXN2,FOXRED2,EIF3S7
chr4 144.4:144.6 USP38,GAB1
chr13 110.6:110.8 ARHGEF7,C13orf16
chrX 86.2:86.4
chr3 62.6:62.8 CADPS
chr10 15.4:15.6 C10orf38,ITGA8
chr7 126.6:127 GRM8,ZNF800,GCC1,ARF5,FSCN3,PAX4
chr3 176.6:177 NAALADL2
chr7 111.8:112 ZNF277P,IFRD1,FLJ39575
chr3 27.2:27.4 NEK10,SLC4A7
chr5 139:139.2 UBE2D2,CXXC5,PSD2,NRG2
chr7 50:50.2 ZPBP
chr11 81:81.2
chr3 169:169.2 SERPINI1,GOLPH4
chr9 15.8:16 C9orf93
chr4 160.4:160.8
chr1 232.8:233 IRF2BP2
chr1 74.6:74.8 TNNI3K,C1orf173
chr18 29.4:29.6
chr2 178.4:178.6 PDE11A
chr16 78.4:78.6
chr13 62:62.2
chr6 32.2:32.4 C6orf10,TNXB,CREBL1,FKBPL,PRRT1,PPT2,EGFL8,AGPAT1,RNF5,AGER,GPSM3,NOTCH4,LOC401252,PBX2
chr1 171.2:171.4 TNFSF18,TNFSF4
chr5 172.8:173 FAM44B
chr4 153:153.2
chr6 105.6:105.8 LIN28B,BVES,POPDC3,PREP
chr7 138.2:138.4 ZC3HAV1L,ZC3HAV1
chr3 197.4:197.6 TM4SF19,FLJ25996,ZDHHC19,OSTalpha,PCYT1A,MGC33212
chr8 11:11.2 C8orf15,MTMR9,AMAC1L2,XKR6
chr9 23:23.2
chr10 73.6:73.8 ASCC1,C10orf104,DDIT4,DNAJB12,CBARA1
chr3 114.4:114.6 BOC,WDR52,CCDC52
chr2 43.6:43.8 THADA,PLEKHH2
chr5 38:38.2
chr2 56.6:56.8
BiakaPygmy
BantuEurope
Mideast
S.AsiaE.Asia
Oceania
America
0.05
0.001
Figure 18: The top 1% of iHS signals in East Asia, ordered from top to bottom in order ofsignificance. See the caption of Figure 1 in the main text for details.
21
chr16 11:11.4 PRM1,KIAA0350,SOCS1,TNP2,PRM3,PRM2,C16orf75,LOC400499
chr2 161.2:161.6chr6 47.6:47.8 GPR115,GPR111,CD2AP
chr10 110:110.2chr12 30.8:31 C1QDC1,TSPAN11
chr6 122.6:122.8 HSF2,SERINC1,PKIB
chr13 87.8:88.2chr5 141:141.2 HDAC3,C5orf16,FCHSD1,CENTD3,PCDH1,DIAPH1
chr4 68.6:68.8 TMPRSS11F,CHR415SYT,TMPRSS11B
chr8 33.4:33.6 FUT10,RBM13,C8orf41,RNF122,DUSP26
chr16 8.4:8.6 C16orf68
chr20 52:52.2 BCAS1,CYP24A1
chr3 158:158.2 FLJ16641
chr7 107.8:108 NRCAM,PNPLA8,THAP5,DNAJB9
chr1 159.8:160.2 FCGR2A,HSPA6,FCGR3A,FCGR2C,FCGR3B,FCGR2B,FCRLA,FCRLB,DUSP12,ATF6,OLFML2B
chr21 39.6:39.8 C21orf87,BRWD1,HMGN1,WRB,C21orf13,SH3BGR,LOC728776
chr6 123:123.2 PKIB,FABP7,SMPDL3A
chr7 100.4:100.6 MUC17,TRIM56,SERPINE1,AP1S1,VGF,FLJ39237,MOGAT3,PLOD3,ZNHIT1
chr6 73:73.2 RIMS1
chr8 95.6:95.8 RAD54B,KIAA1429,RBM35A,DPY19L4
chr3 21.2:21.4 ZNF659
chr6 54.6:55 FAM83B
chr12 30.2:30.4chr12 3.6:3.8 PRMT8,EFCAB4B,PARP11
chr3 24.8:25chr1 196.4:196.6 NEK7
chr5 80.8:81.2 SSBP2
chr21 40:40.2 B3GALT5,PCP4,LOC150084
chr5 153.6:153.8 GALNT10,SAP30L,HAND1
chr6 122.2:122.4chr11 69:69.2 CCND1,FLJ42258,ORAOV1,FGF19
chr2 3.2:3.4 TSSC1,TTC15
chr17 32.4:32.6 LHX1,AATF,ACACA
chr22 48.4:48.6 C22orf34,BRD1,ZBED4
chr2 54.8:55.2 SPTBN1,RTN4,FLJ42562
chr11 6.6:6.8 KIAA0409,ILK,TAF10,DCHS1,MRPL17,OR2AG2,OR2AG1,OR6A2,OR10A5,OR10A2,TPP1
chr12 73.6:73.8 KCNC2
chr7 131.6:131.8 PLXNA4B
chr2 17.8:18 SMC6,FLJ40869,KCNS3
chr6 119.2:119.4 MCMDC1,ASF1A,C6orf60
chr12 107.8:108 SSH1,DAO,SVOP,USP30,ALKBH2,UNG
chr2 36:36.2chr4 143.8:144
chr14 100:100.2 WDR25,KIAA1446,C14orf70
chr5 107.2:107.4 FBXL17
chr11 56.6:56.8 LRRC55,AGTRL1,TNKS1BP1
chr12 26.2:26.6 BHLHB3,SSPN,ITPR2
chr2 160.8:161 ITGB6,RBMS1
chr12 46.2:46.4 FLJ21908,P11,RAPGEF3
chr2 7:7.2 RNF144,RSAD2
chr6 154.4:154.6 OPRM1,PIP3−E
chr17 34.4:34.6 FBXO47,PLXDC1,CACNB1,RPL19,STAC2
chr18 32.6:32.8 FHOD3,C18orf10,KIAA1328
chr15 34:34.2chr10 31.2:31.4 ZNF438
chr17 36.2:36.4 KRT28,KRT40,KRT25,KRT26,KRT27,KRT10,KRT12,KRT20,KRT23,KRT39,KRTAP3−3,KRTAP3−2,KRTAP3−1,KRTAP1−5,KRTAP1−3,TMEM99
chr2 26.4:26.6 GPR113,SELI,C2orf39,OTOF,HADHB
chr2 52:52.2chr1 197.2:197.4chr5 164.6:164.8
chr5 154.8:155chr3 24.2:24.4 THRB
chrX 8.4:8.6 VCX−C,KAL1
chr2 169.4:169.6 NOSTRIN,SPBC25,G6PC2,ABCB11,DHRS9
chr6 47:47.2 GPR116,GPR110
chr15 56.2:56.4 AQP9
chr2 26.8:27 CENPA,KCNK3,DPYSL5,MAPRE3,C2orf18
chr4 60:60.2chr6 119.6:119.8 MAN1A1
chr1 89.6:89.8 GBP6,LRRC8B
chr4 164:164.2chr12 7.6:7.8 APOBEC1,GDF3,DPPA3,CLEC4C,NANOG
chr3 1.6:2chr7 122.6:122.8 SLC13A1
chr20 2.8:3 PTPRA,FAM113A,VPS16,GNRH2,MRPS26,OXT,AVP,UBOX5
chr16 78.6:78.8chr2 160.4:160.6 CD302,LY75,PLA2R1
chr15 50.8:51 KIAA1370,ONECUT1
chr6 35:35.2 C6orf107,TAF11,ANKS1A,TCP11
chr6 111.6:111.8 SLC16A10,KIAA1919,REV3L
chr13 37.4:37.6chr4 129.4:129.6 LARP2,PGRMC2
chr6 46.6:46.8 CYP39A1,TDRD6,PLA2G7,SLC25A27
chr15 56.8:57 ADAM10,SLTM,FAM63B
chr1 164.8:165
BiakaPygmy
BantuEurope
Mideast
S.AsiaE.Asia
Oceania
America
0.05
0.001
Figure 19: The top 1% of iHS signals in the Americas, ordered from top to bottom in order ofsignificance. See the caption of Figure 1 in the main text for details.
22
chr8 63.8:64 FAM77D
chr3 67.6:67.8 SUCLG2
chr2 165.2:165.6 GRB14,COBLL1,FLJ39822
chr2 126:126.2chr14 69.4:69.6 SMOC1,SLC8A3
chr5 61.2:61.4chr6 29.4:29.6 OR5U1,OR5V1,OR12D3,OR12D2,OR11A1,OR10C1,OR2H1,MAS1L
chr3 162.6:162.8 C3orf57,LOC131149
chr12 92.8:93 CRADD
chr2 165.8:166.2 SCN2A,SCN3A,FAM130A2
chr8 121.6:121.8 MTBP,SNTB1
chr9 1.6:1.8chr2 3.2:3.6 TSSC1,TTC15,ADI1,RNASEH1,RPS7,COLEC11
chr5 63.8:64 RGS7BP,P18SRP
chr20 5.8:6 C20orf196,CHGB,CGI−09,MCM8,CRLS1,C20orf75,C20orf42
chr1 183:183.2 EDEM3,FAM129A
chr2 22.6:22.8chr1 162.4:162.6
chr4 14.6:14.8 CPEB2
chr18 24.4:24.6chr15 96.8:97 FLJ39743,IGF1R
chr13 43.6:43.8 C13orf21
chr6 132.2:132.6 CTGF,ENPP1
chr15 51.6:51.8 WDR72
chr9 126.8:127 C9orf126,PPP6C,RABEPK,HSPA5
chr10 76.4:76.6 DUPD1,DUSP13,SAMD8,VDAC2,MYST4
chr13 110.4:110.6 ANKRD10,ARHGEF7
chr16 77.2:77.6 WWOX
chr1 70.2:70.4 LRRC40,SFRS11,LRRC7
chr3 162.2:162.4 PPM1L,B3GALNT1,NMD3
chr8 14:14.2 SGCZ
chr6 39.6:39.8 KIF6
chr13 46:46.2 LRCH1,ESD
chr8 63.2:63.6 FAM77D
chr4 113.4:113.6 C4orf16,TIFA,ALPK1
chr8 5.8:6chr7 120.4:120.8 ING3,FLJ21986,WNT16,FAM3C
chr6 160.2:160.4 IGF2R,PNLDC1,MAS1
chr2 178:178.2 PDE11A,AGPS,TTC30A,TTC30B
chr17 61.2:61.4 CCDC46
chr14 68.4:68.6 ACTN1,WDR22
chr1 185.4:185.6chr17 40.2:40.4 ADAM11,DBF4B,HIGD1B,EFTUD2,CCDC103,GFAP,C1QL1,GJA7,LOC146909
chr2 212.8:213 ERBB4
chr10 80:80.2chr2 2.8:3
chr8 17.8:18 FGL1,PCM1,ASAH1
chr9 125:125.4 CRB2,STRBP,DENND1A
chr6 108.8:109 LACE1,FOXO3A
chr10 49.8:50 LRRC18,C10orf72
chr2 81.8:82chr3 38.4:38.6 XYLB,ENDOGL1,ACVR2B,SCN5A
chr2 212.4:212.6 ERBB4
chr5 64.4:64.6 SDCCAG10,ADAMTS6
chr3 26.6:26.8 LRRC3B
chr16 50.8:51 TNRC9
chr13 101.6:101.8 FGF14
chr1 182.4:182.6 C1orf21
chr1 207:207.2chr1 148.8:149 ECM1,ADAMTSL4,C1orf138,MCL1,ENSA,GOLPH3L,HORMAD1,CTSS,CTSK,ARNT
chr2 151.6:151.8 RBM43,NMI
chr4 60.6:60.8chr7 124.8:125
chr10 44.8:45 RASSF4,C10orf10,C10orf25,ZNF22
chrX 12.4:12.6 FRMPD4
chr9 0.6:1 ANKRD15,DMRT1,DMRT3,DMRT2
chr22 41:41.2 NFAM1,SERHL,CGI−96
chr5 114.8:115 FEM1C,TICAM2,TMED7
chr20 40:40.2 PTPRT
chr3 171.4:171.6 PHC3,PRKCI,SKIL,CLDN11
chr2 198.2:198.4 RFTN2,MARS2,BOLL
chr7 103.6:103.8 LHFPL3,ORC5L
chr7 19.2:19.4 FERD3L
chr11 33.6:33.8 C11orf69,CD59,FBXO3,LMO2
chr5 169.6:169.8 LCP2,KCNIP1,KCNMB1
chr1 175.4:175.6 ASTN1,FAM5B
chr22 41.6:41.8 ARFGAP3,PACSIN2,TTLL1,BIK
chr2 213.6:213.8 IKZF2
chr10 43.4:43.6 ZNF239,ZNF485,ZNF32
chr6 56.2:56.4 COL21A1,DST
chr12 41.8:42 ADAMTS20
chr12 119.4:119.6 COQ5,COX6A1,TRIAP1,15E1.2,SFRS9,DYNLL1,RNF10,POP5,CABP1,KIAA0152,ACADS,MGC5139
chr18 9.2:9.4 ANKRD12,TWSG1
chr20 17.2:17.4 PCSK2,BFSP1
chr10 76:76.2 ADK
chr5 58.4:58.6 PDE4D
chr7 23.8:24 STK31
BiakaPygmy
BantuEurope
Mideast
S.AsiaE.Asia
Oceania
America
0.05
0.001
Figure 20: The top 1% of iHS signals in Oceania, ordered from top to bottom in order of significance.See the caption of Figure 1 in the main text for details.
23
chr13 24.2:24.4 ATP12A,CENPJ,RNF17
chr20 34.8:35 NDRG3,DSN1,C20orf117,C20orf118,SAMHD1
chr17 0.6:0.8 VPS53,FAM57A,C17orf25,RNMTL1,NXN,TIMM22,GEMIN4
chr6 164.6:164.8chr19 47:47.2 CEACAM6,LYPD4,RPS19,ARHGEF1,RABAC1,ATP1A3,GRIK5,DMRTC2,CEACAM3,CD79A
chr6 52:52.2 PKHD1,IL17A,IL17F,MCM3
chr3 121.8:122 NDUFB4,GTF2E1,HGD,RABL3
chr14 84.6:84.8chr11 18.6:18.8 SPTY2D1,TMEM86A,IGSF22,PTPN5,UEVLD
chr17 21.2:21.6 MAP2K3,KCNJ12
chr11 63:63.2 HRASLS5,LGALS12,RARRES3,HRASLS2,HRASLS3,DKFZP564J0863,RTN3
chr13 59.6:59.8 DIAPH3
chr1 207:207.2chr2 59:59.2
chr3 194.2:194.4 HRASLS
chr19 45.6:45.8 PLD3,HIPK4,SERTAD1,SERTAD3,BLVRB,SHKBP1,PRX,SPTBN4,LTBP4
chr12 106.2:106.4 BTBD11
chr18 44.8:45 DYM
chr17 58.8:59 CYB561,ACE,KCNH6,CCDC44,WDR68
chr10 92:92.2chr13 58.6:58.8
chr10 86:86.2 LRRC21,LRRC22,PCDH21,RGR,KIAA1128
chr10 42.8:43 RASGEF1A,RET,GALNACT−2
chr3 148.4:148.6 ZIC4,ZIC1
chr22 34:34.2 HMG2L1,TOM1,HMOX1,MCM5
chr10 12.4:12.6 CAMK1D
chr1 115.6:115.8 NGFB
chr21 43.6:43.8 SNF1LK,FLJ41733,C21orf125,HSF2BP
chr12 54.6:54.8 IKZF4,WIBG,DGKA,SILV,CDK2,RAB5B,SUOX,RPS26,ERBB3,RPL41,ZC3H10,FAM62A,MYL6B,MYL6,SMARCC2,PA2G4
chr6 72.4:72.6chr6 158.6:158.8 TULP4
chr2 105.2:105.4 GPR45,TGFBRAP1,C2orf49,FHL2
chr7 96.4:96.6 DLX6,DLX5,ACN9
chr3 185.4:185.6 DVL3,AP2M1,ABCF3,ALG3,MGC2408,ECE2,CAMK2N2,PSMD2,EIF4G1,C3orf40,CLCN2,POLR2H,THPO,CHRD
chr14 90:90.2 TTC7B
chr7 153.4:153.6 DPP6
chr16 86.4:86.6 KLHDC4,SLC7A5,CA5A,BANP
chrX 41.4:41.8 CASK,GPR34,GPR82
chrX 33.2:33.4 DMD
chr7 38.8:39 VPS41,POU6F2
chr20 16.4:16.6 C20orf23
chr8 106.4:106.6 ZFPM2
chr7 45.2:45.4 RAMP3
chr17 52.4:52.6 AKAP1,COIL,SCPEP1
chr11 43.4:43.6 TTC17
chr17 76:76.2 KIAA1303,RNF213,FLJ35220,NPTX1
chr8 4.8:5 CSMD1
chr19 48.4:48.6 PSG5,PSG4,PSG9,TEX101,CD177
chr5 60.8:61 FLJ37543
chr1 113.8:114.2 MAGI3,PHTF1,RSBN1,PTPN22,C1orf178,AP4B1,DCLRE1B
chr7 36.4:36.6 KIAA0895,ANLN,AOAH
chr1 39.2:39.4 RHBDL2,C1orf108,NDUFS5,MACF1
chr2 49.8:50 NRXN1
chr12 28:28.2 PTHLH
chr7 106.4:106.8 PRKAR2B,HBP1,COG5
chr1 177.2:177.4 RALGPS2,FAM20B,ABL2,TOR3A
chr8 26.6:26.8 ADRA1A,DPYSL2
chr2 50.8:51 NRXN1
chr8 59.6:59.8 CYP7A1,SDCBP,NSMAF
chr3 45.6:45.8 LARS2,SACM1L,SLC6A20,LZTFL1,LIMD1
chr16 4.2:4.4 TFAP4,Magmas,CORO7,VASN,DNAJA3,GLIS2
chr9 134.8:135 C9orf9,TSC1,GFI1B,GTF3C5,CEL,RALGDS,GBGT1
chr17 3.4:3.6 TRPV1,CTNS,TRPV3,CARKL,TAX1BP3,TMEM93,P2RX5,ITGAE,GSG2
chr11 13.6:13.8 MLSTD2
chr19 0.6:0.8 HCN2,POLRMT,FGF22,FLJ45684,RNF126,PRSSL1,C19orf21,PTBP1,PRG2,AZU1,PRTN3,ELA2,CFD,THRAP5,C19orf22,FSTL3,PALM
chr1 82.4:82.8chr12 97.6:97.8 IKIP,APAF1,ANKS1B
chr19 5.2:5.4 PTPRS,ZNRF4
chr11 132.4:132.6 OPCML
chr10 15.8:16.2 ITGA8,C10orf97
chr7 62.2:62.4chr18 40.8:41 SETBP1
chr6 26.4:26.6 HIST1H4G,HIST1H3F,HIST1H2BH,HIST1H3G,HIST1H2BI,HIST1H4H,BTN3A2,BTN2A2,BTN3A1,BTN2A3,BTN3A3,BTN2A1,BTN1A1,HMGN4
chr19 50.4:50.6 TRAPPC6A,EXOC3L2,MARK4,CKM,ERCC2,PPP1R13L,CD3EAP,ERCC1,BLOC1S3,KLC3
chr11 76.4:76.6 PHCA,CAPN5,OMP,GDPD4,B3GNT6,MYO7A
chr9 25:25.2chr14 100.2:100.4 C14orf70,DLK1
chr7 23:23.2 FAM126A,KLHL7,NUPL2
chr4 109.2:109.4 LEF1,HADH
chrX 62.8:63 ARHGEF9
chr20 37.8:38chrX 8:8.2 VCX2
chr4 180.4:180.6chr4 147:147.2 LOC152485
chr2 213.6:213.8 IKZF2
chr22 26.4:26.6 MN1,PITPNB
chr10 104:104.2 NFKB2,ELOVL3,PITX3,GBF1,PSD,FBXL15,CUEDC2,C10orf95,TMEM180,ACTR1A
chr1 159.6:159.8 SDHC,C1orf192,FCGR2A,HSPA6,FCGR3A,FCGR2C
chr1 11.6:11.8 FBXO2,FBXO44,FBXO6,MAD2L2,C1orf187,MTHFR,CLCN6,NPPA,NPPB,AGTRAP
chr6 151:151.2 PLEKHG1,MTHFD1L
chr10 91:91.2 LIPA,IFIT2,IFIT3,IFIT1L,IFIT5,SLC16A12,IFIT1,CH25H
chr6 144.2:144.4 PHACTR2,LTV1,PLAGL1
chr14 100.8:101chr7 44.2:44.6 GCK,YKT6,CAMK2B,NPC1L1,DDX56,TMED4,OGDH,NUDCD3
chr17 68.8:69 C17orf80,CDC42EP4,SDK2
chr3 156.2:156.4 MME,FLJ46120
chr11 29.8:30 KCNA4
chr11 11.4:11.6 GALNTL4
chr7 0.8:1 HEATR2,C7orf20,CENTA1,CYP2W1,MGC11257,FLJ44124,UNC84A,COX19
chr11 115.8:116chr11 121.6:121.8
chr18 62.4:62.6 CDH19
chr14 74.8:75 FOS,JDP2
chr21 34:34.2 ITSN1,ATP5O
chr10 9.6:9.8chr6 165.4:165.6 C6orf118
chr14 73.2:73.4 ACOT6,DNAL1,PNMA1,C14orf43,ZADH1,ZNF410
chr5 91.8:92chr12 16.6:16.8 LMO3
chr7 17.6:17.8 SNX13
chr9 138.4:138.6 SNAPC4,GPSM1,CARD9,SDCCAG3,PMPCA,INPP5E,C9orf163,NOTCH1,LOC728489,KIAA0310
chr22 20.2:20.4 LOC220686,LOC375133,UBE2L3,LOC150223,CCDC116,SDF2L1,PPIL2,YPEL1,MAPK1
chr11 61.2:61.4 C11orf11,C11orf9,C11orf10,FEN1,FADS1,FADS2,FADS3,RAB3IL1
chr9 99.6:99.8 ANP32B,C9orf156,FOXE1,HEMGN
chr17 42.6:42.8 CDC27,MYL4,ITGB3,C17orf57
chr9 27.4:27.6 IFNK,MOBKL2B,C9orf72
chr11 34.2:34.4 ABTB2,CAT
chr1 41.2:41.4 CTPS,SLFNL1,SCMH1
chr11 107.2:107.4 SLC35F2,RAB39,CUL5
chr7 43.4:43.6 C7orf44,HECW1,STK17A
chr2 44:44.2 ABCG8,LRPPRC,PPM1B
chr15 82.6:82.8 KIAA1920
chr8 135.2:135.4
BiakaPygmy
BantuEurope
Mideast
S.AsiaE.Asia
Oceania
America
0.05
0.001
Figure 21: The top 1% of XP-EHH signals in the Bantu, ordered from top to bottom in order ofsignificance. See the caption of Figure 1 in the main text for details.
24
chr6 164.6:164.8chr10 9.6:9.8chr17 0.6:0.8 VPS53,FAM57A,C17orf25,RNMTL1,NXN,TIMM22,GEMIN4
chr6 52:52.2 PKHD1,IL17A,IL17F,MCM3
chr8 106.4:106.6 ZFPM2
chr11 18.6:18.8 SPTY2D1,TMEM86A,IGSF22,PTPN5,UEVLD
chr16 86.4:86.6 KLHDC4,SLC7A5,CA5A,BANP
chr7 106.2:106.4 PIK3CG
chr10 0.6:0.8 DIP2C,C10orf108,LARP5
chr19 52:52.4 SLC1A5,AP2S1,GRLF1,NPAS1,TMEM160,SAE1,BBC3,FKRP
chr1 82.4:82.6chr13 59.6:59.8 DIAPH3
chr11 34.2:34.4 ABTB2,CAT
chr13 107.6:107.8 LIG4,ABHD13,TNFSF13B
chr3 115.4:115.6 DRD3,ZNF80,VSIG9,ZBTB20
chr11 29.8:30 KCNA4
chr9 115:115.2 RGS3,SLC31A2,SLC31A1,CDC26,PRPF4,RNF183,WDR31,BSPRY,HDHD3,ALAD,POLE3,C9orf43
chr18 52:52.2 FLJ45743
chr22 38.4:38.6 CACNA1I,ENTHD1,GRAP2
chr18 44.8:45 DYM
chr14 100.2:100.4 C14orf70,DLK1
chr9 25:25.2chr1 198.6:198.8 ZNF281,KIF14
chr20 60.6:60.8 FLJ30313,C20orf166,SLCO4A1,NTSR1
chr8 126.8:127chr3 2.4:2.6 CNTN4
chr5 178.2:178.4 GRM6,ZNF354B,ZFP2,ZNF454,ZNF354C
chr11 32.4:32.6 WT1,WIT1,PCID1,CCDC73
chr15 49.4:49.6 GLDN,CYP19A1,DMXL2
chr16 27.6:27.8 KIAA0556,GSG1L
chr17 58.8:59 CYB561,ACE,KCNH6,CCDC44,WDR68
chr8 0.2:0.4 C8orf42,ZNF596,FBXO25
chr4 4.6:4.8 STX18
chr19 48.4:48.6 PSG5,PSG4,PSG9,TEX101,CD177
chr8 125.4:125.6 TMEM65,TRMT12,RNF139,TATDN1,NDUFB9,MTSS1
chr6 20:20.2 MBOAT1
chr7 139.2:139.4 TBXAS1,PARP12,KIAA1718
chr11 63:63.2 HRASLS5,LGALS12,RARRES3,HRASLS2,HRASLS3,DKFZP564J0863,RTN3
chrX 91.6:91.8 PCDH11X
chrX 115:115.2 AGTR2
chr14 94.6:94.8 DICER1,FLJ45244,CLMN
chr19 56.8:57 ZNF175,SIGLEC5,HAS1,FPR1,FPRL1,FPRL2
chr22 15.4:15.6 CESK1,XKR3
chr9 134.8:135 C9orf9,TSC1,GFI1B,GTF3C5,CEL,RALGDS,GBGT1
chr5 177.4:177.6 LOC653316,PROP1,N4BP3,RMND5B,NOLA2,HNRPAB,AGXT2L2,COL23A1,LOC653314
chr17 76.6:76.8 KIAA1303,AZI1,CHMP6,BAIAP2,FLJ44861,C17orf56,MGC15523,AATK
chr6 67.2:67.4chr15 23.4:23.6 ATP10A
chr10 104:104.2 NFKB2,ELOVL3,PITX3,GBF1,PSD,FBXL15,CUEDC2,C10orf95,TMEM180,ACTR1A
chr11 94.8:95chr11 13.6:13.8 MLSTD2
chr11 61.2:61.4 C11orf11,C11orf9,C11orf10,FEN1,FADS1,FADS2,FADS3,RAB3IL1
chr3 195.4:195.6 GP5,LRRC15,CPN2
chr9 132.8:133 LAMC3,ABL1,P518,FIBCD1,C9orf58,NUP214
chr13 106.6:106.8 LOC728215
chr3 121.8:122 NDUFB4,GTF2E1,HGD,RABL3
chr13 89.8:90chr10 12.4:12.6 CAMK1D
chr19 45.6:45.8 PLD3,HIPK4,SERTAD1,SERTAD3,BLVRB,SHKBP1,PRX,SPTBN4,LTBP4
chr12 66.2:66.4 DYRK2
chr3 156.2:156.4 MME,FLJ46120
chr17 21.2:21.6 MAP2K3,KCNJ12
chr7 153:153.2 DPP6,FLJ16734
chr2 11.8:12 LPIN1
chr1 238:238.2 CHRM3
chr22 34:34.2 HMG2L1,TOM1,HMOX1,MCM5
chr1 1.8:2.2 GNB1,CALML6,TMEM52,LOC339457,GABRD,PRKCZ,SKI,MORN1,C1orf86,KIAA1751
chr9 112.8:113 EDG2
chr2 183.4:183.6 DNAJC10,FRZB,NCKAP1
chr13 58.6:58.8chr16 64:64.2
chr20 16.4:16.6 C20orf23
chr3 98.8:99 ARL6,EPHA6
chr1 57:57.2 C1orf168,C8A,C8B,DAB1
chr16 31.2:31.6 ITGAM,ITGAX,ITGAD,COX6A2,ARMC5,TGFB1I1,SLC5A2,C16orf58,ERAF
chr6 26.4:26.6 HIST1H4G,HIST1H3F,HIST1H2BH,HIST1H3G,HIST1H2BI,HIST1H4H,BTN3A2,BTN2A2,BTN3A1,BTN2A3,BTN3A3,BTN2A1,BTN1A1,HMGN4
chr11 0.6:0.8 CEND1,C11orf35,RASSF7,KIAA1542,SCT,DRD4,DEAF1,EPS8L2,TALDO1,SLC25A22,LRDD,RPLP2,PNPLA2,EFCAB4A,CD151,POLR2L,TSPAN4,IRF7,MUCDHL,TMEM80,PDDC1
chr8 59.2:59.4 C8orf72
chr6 24:24.2 NRSN1
chr17 27.8:28 PSMD11,CDK5R1,MYO1D
chr7 106.6:106.8 PRKAR2B,HBP1,COG5
chr14 43.6:43.8chrX 41.6:41.8 CASK
chr1 171.2:171.4 TNFSF18,TNFSF4
chr2 105.2:105.4 GPR45,TGFBRAP1,C2orf49,FHL2
chrX 102.8:103 TCEAL3,TCEAL1,MORF4L2,TMEM31,PLP1,RAB9B
chr15 76.4:76.6 DNAJA4,WDR61,CRABP1,IREB2,LOC123688,PSMA4,CHRNA5
chr17 9:9.2 NTN1,STX8
chr1 12.2:12.4 TNFRSF1B,VPS13D
chr4 13:13.2 RAB28,BAPX1,FAM44A
chr12 29.8:30 TMTC1
chr5 56.8:57 DKFZp686D0972
chr20 34.8:35 NDRG3,DSN1,C20orf117,C20orf118,SAMHD1
chr11 133.2:133.4 SPATA19,JAM3
chr19 1:1.2 GRIN3B,C19orf6,CNN2,ABCA7,HMHA1,POLR2E,SBNO2,STK11,C19orf26,ATP5D,MIDN,C19orf23,CIRBP,C19orf24,EFNA2,GPX4
chr11 113.8:114 FAM55D,C11orf71,RBM7,REXO2,FAM55A
chr2 171:171.2 MYO3B
chr18 40.8:41 SETBP1
chr10 12:12.2 C10orf47,UPF2,DHTKD1,SEC61A2,NUDT5
chr6 148.8:149 SASH1
chr16 55.4:55.6 NLRC5,NUP93,SLC12A3,HERPUD1,CETP
chr19 5.4:5.6 ZNRF4,PLAC2,SAFB,P117,HSD11B1L,RPL36,LONP1,SAFB2
chr8 109.6:109.8 TTC35
chr15 20.4:20.6 TUBGCP5,CYFIP1,NIPA2,NIPA1
chr17 64.8:65 ABCA10,ABCA5,MAP2K6
chr7 5.2:5.4 WIPI2,FBXL18,SLC29A4,KIAA1856
chr4 114.4:114.6 ANK2,CAMK2D
chr19 38:38.2 SLC7A9,CCDC123,C19orf40,RHPN2
chr12 55.8:56 KIAA0286,STAT6,LRP1,NXPH4,SHMT2,NDUFA4L2,STAC3,R3HDM2,NAB2
chr1 158.4:158.6 ATP1A2,ATP1A4,CASQ1,PEA15,WDR42A,PEX19,COPA,NCSTN,NHLH1,VANGL2
chr3 9.2:9.4 SRGAP3,THUMPD3,SETD5
chr5 126.2:126.4 LMNB1,MARCH3
chr12 29:29.2chr2 111.8:112chr6 155:155.2 RBM16
chr18 5.2:5.4 ZFP161,EPB41L3
chr9 83.4:83.6 TLE1
chr12 102.6:102.8 STAB2,NT5DC3,HSP90B1
chr1 39.2:39.4 RHBDL2,C1orf108,NDUFS5,MACF1
chr3 12.8:13 TMEM40,RPL32,IQSEC1,CAND2
chr11 43.4:43.6 TTC17
chr7 155.4:155.6chr19 0.4:0.6 MADCAM1,C19orf19,CDC34,GZMM,BSG,HCN2,POLRMT,FGF22,FLJ45684,RNF126,PRSSL1,C19orf20,FSTL3
chr21 43.2:43.4 WDR4,NDUFV3,PKNOX1,CBS,U2AF1
chr16 53.2:53.4
BiakaPygmy
BantuEurope
Mideast
S.AsiaE.Asia
Oceania
America
0.05
0.001
Figure 22: The top 1% of XP-EHH signals in the Biaka Pygmies, ordered from top to bottom inorder of significance. See the caption of Figure 1 in the main text for details.
25
chr21 16.8:17 C21orf34
chr15 46:46.4 SLC24A5,MYEF2,SLC12A1,DUT
chr17 60.6:61 RGS9,AXIN2
chr9 90:90.4 SPIN1,C9orf121
chr3 131.4:131.8 FLJ35880
chr12 87.4:87.8 KITLG
chr8 140:140.2 COL22A1
chr10 65.4:65.8chr17 56.2:56.6 BCAS3
chr7 119.6:120 KCND2
chr18 11.2:11.4chr14 61:61.2 PRKCH,HIF1A
chr10 83.6:83.8 NRG3
chr4 82:82.4 C4orf22,BMP3,PRKG2
chr1 35.4:35.8 SFPQ,ZMYM4,KIAA0319L,NCDN,TFAP2E,PSMB2,ZMYM1
chr2 238:238.2 COL6A3,PRLH,RAB17,MLPH
chr15 67.4:67.8 GLCE,PAQR5,KIF23,RPLP1,LOC729416
chr18 19.6:20 LAMA3,CABYR,OSBPL1A,C18orf17
chr6 0:0.2 DUSP22,FLJ43763
chr4 32.6:33chr5 109.6:110
chr5 21.8:22 CDH12
chr7 18.6:18.8 HDAC9
chr3 72.6:72.8 RYBP
chr5 26.4:26.8chr3 25.8:26 NGLY1,OXSM
chr4 55.8:56 SRD5A2L,TMEM165,CLOCK
chr3 176.6:176.8 NAALADL2
chr5 74.4:74.8 GCNT4,HMGCR,COL4A3BP,POLK
chr3 31.2:31.6 STT3B
chr9 3.2:3.4 RFX3
chr12 2.6:2.8 FKBP4,ITFG2,NRIP2,FOXM1,CACNA1C
chrX 110:110.4 PAK3,CAPN6,DCX
chr4 172.6:172.8chr20 58.2:58.4 LOC284757
chr4 5.2:5.4 STK32B
chr14 62.8:63 RHOJ,GPHB5,PPP2R5E
chr20 48.8:49 PARD6B,BCAS4,ADNP,DPM1,MOCS3
chr22 20.6:20.8 MAPK1,PPM1F,TOP3B
chr15 89.8:90chr10 84:84.2 NRG3
chr18 7.4:7.8 PTPRM
chr20 52.4:52.6 DOK5
chr6 73.8:74 C6orf148,KCNQ5
chr1 244:244.2 SMYD3
chr1 36:36.4 FLJ38984,CLSPN,EIF2C4,EIF2C1,EIF2C3,TEKT2,ADPRHL2,COL8A2,TRAPPC3,MAP7D1
chr2 178:178.4 PDE11A,AGPS,TTC30A,TTC30B
chr4 60.8:61.2chr17 55.6:56 CA4,USP32,C17orf64,APPBP2,PPM1D
chr5 75:75.4 C5orf37,SV2C
chr2 152.2:152.4 NEB,ARL5A,CACNB4
chr6 14.8:15chr12 57.6:57.8 LRIG3
chr8 16.2:16.4chr11 64:64.2 SLC22A11,SLC22A12,NRXN2
chr3 3.8:4 LRRN1
chr22 45:45.2 FLJ20699,PPARA,LOC150383,PKDREJ,GTSE1,TRMU,CELSR1
chr6 143:143.2 HIVEP2
chr10 22.4:22.8 COMMD3,BMI1,SPAG6
chr11 41.8:42chr21 29.8:30.2 GRIK1
chr3 192:192.2chr7 33.6:33.8 BBS9
chr10 118:118.4 GFRA1,C10orf96,PNLIPRP3,PNLIP,PNLIPRP1,C10orf82,PNLIPRP2,HSPA12A
chrX 36:36.2 CXorf59
chr17 51.4:51.6 ANKFN1
chr15 46.6:46.8 CEP152,FBN1
chr7 37:37.2 ELMO1
chr16 64.6:64.8chr5 90.4:90.6 GPR98
chr3 100.4:100.8 COL8A1
chr2 167.6:168 CMYA3
chr4 14.2:14.4chr8 18.6:18.8 PSD3
chr4 33.2:33.6chr15 27:27.4 APBA2,NDNL2
chr4 29.4:29.8chr6 108:108.2 SCML4,FLJ10159
chr13 73.6:73.8 KLF12
chr19 7.2:7.6 ARHGEF18,PEX11G,C19orf45,ZNF358,MCOLN1,XAB2,PCP2,STXBP2,RETN,PNPLA6,C19orf59,INSR,KIAA1543
chr1 228:228.2chr1 192.4:192.6chr6 105.6:105.8 LIN28B,BVES,POPDC3,PREP
chr1 160.2:160.4 ATF6,OLFML2B,NOS1AP
chr18 64.8:65 CCDC102B
chr6 75.6:75.8chr6 124:124.2 TCBA1,TRDN
chr15 57.2:57.4 RNF111,CCNB2,MYO1E,LDHAL6B
chr2 120.8:121 RALB,INHBB
chr2 222.2:222.4chrX 98.4:98.6chr1 234.8:235 LGALS8,HEATR1,ACTN2,MTR
BiakaPygmy
BantuEurope
Mideast
S.AsiaE.Asia
Oceania
America
0.05
0.001
Figure 23: The top 1% of XP-EHH signals in Europe, ordered from top to bottom in order ofsignificance. See the caption of Figure 1 in the main text for details.
26
chr21 16.8:17 C21orf34
chr15 46:46.4 SLC24A5,MYEF2,SLC12A1,DUT
chr8 140:140.2 COL22A1
chr22 45:45.2 FLJ20699,PPARA,LOC150383,PKDREJ,GTSE1,TRMU,CELSR1
chr6 0:0.2 DUSP22,FLJ43763
chr14 62.6:63 KCNH5,RHOJ,GPHB5,PPP2R5E
chr17 56:56.4 APPBP2,PPM1D,BCAS3
chr5 26.4:26.8chr14 61:61.2 PRKCH,HIF1A
chr8 139.6:139.8 C8ORFK32,COL22A1
chr12 87.2:87.6 KITLG
chr3 25.6:26 RARB,TOP2B,NGLY1,OXSM
chr7 119.4:119.8 KCND2
chr11 8:8.2 EIF3S5,TUB,RIC3,LMO1
chr10 65.4:65.8chr15 46.6:46.8 CEP152,FBN1
chr5 109.6:110chr2 238:238.2 COL6A3,PRLH,RAB17,MLPH
chr3 31.2:31.6 STT3B
chr18 55.8:56chr6 108:108.2 SCML4,FLJ10159
chr15 27:27.4 APBA2,NDNL2
chr5 23.2:23.6 PRDM9
chr20 52.4:52.6 DOK5
chr6 123.8:124.2 TCBA1,TRDN
chr17 52.6:53 AKAP1,MSI2
chr10 22.2:22.6 COMMD3,DNAJC1
chr9 1.8:2 SMARCA2
chr19 7.2:7.6 ARHGEF18,PEX11G,C19orf45,ZNF358,MCOLN1,XAB2,PCP2,STXBP2,RETN,PNPLA6,C19orf59,INSR,KIAA1543
chrX 110:110.4 PAK3,CAPN6,DCX
chrX 35.8:36.2 CXorf59,CXorf22
chr10 118:118.4 GFRA1,C10orf96,PNLIPRP3,PNLIP,PNLIPRP1,C10orf82,PNLIPRP2,HSPA12A
chr8 17.6:17.8 MTUS1,FGL1,PCM1
chr21 29.8:30.2 GRIK1
chr3 131.6:131.8 FLJ35880
chr1 35.2:35.6 SFPQ,ZMYM4,ZMYM1,ZMYM6
chr1 35.8:36.2 KIAA0319L,NCDN,TFAP2E,PSMB2,FLJ38984,CLSPN,EIF2C4,EIF2C1,EIF2C3
chr16 77:77.2 WWOX
chr7 33.6:33.8 BBS9
chr12 57.6:57.8 LRIG3
chr3 26.2:26.4chr15 67.6:67.8
chr12 124.6:124.8 TMEM132B
chr11 64:64.4 SLC22A11,SLC22A12,NRXN2,RASGRP2,PYGM,SF1,MAP4K2,MEN1,CDC42BPG,EHD1,KIAA0404,PPP2R5B
chr1 65:65.2 RAVER2,JAK1
chr9 32.6:32.8 NDUFB6,TAF1L,LOC401498
chr1 192.2:192.6chr3 112.6:112.8 CD96,ZBED2
chr6 14.8:15chr18 19.8:20 LAMA3,CABYR,OSBPL1A,C18orf17
chr6 73.8:74 C6orf148,KCNQ5
chr10 25.8:26 GPR158
chr3 113:113.2 TMPRSS7,PLCXD2,PHLDB2,ABHD10,TAGLN3
chr3 100.4:100.8 COL8A1
chr10 22.8:23 PIP5K2A
chr5 21.8:22 CDH12
chr4 55.8:56 SRD5A2L,TMEM165,CLOCK
chr18 7.4:7.6 PTPRM
chr4 172.6:172.8chr9 90.2:90.4 SPIN1,C9orf121
chr2 222.2:222.4chr17 60.6:60.8 RGS9
chr20 21.8:22chr16 1.8:2 RNF151,MAPK8IP3,NME3,MRPS34,EME2,SPSB3,NUBP2,IGFALS,FAHD1,C16orf73,SEPX1,RPL3L,NDUFB10,RPS2,TBL3,NOXO1,GFER,SYNGR3,ZNF598,SLC9A3R2,NTHL1,HAGH,TSC2,LOC91561,HS3ST6
chr13 103:103.2chr9 107:107.2 SLC44A1
chr2 213:213.2 ERBB4
chr10 83.6:84 NRG3
chr3 111.2:111.4chr13 33.4:33.6 RFC3
chr4 60.8:61chr5 19.6:19.8 CDH18
chr20 15.6:15.8 C20orf133
chr1 246:246.2 OR5AT1,OR11L1,OR2W3,OR2T8,OR2L13,OR2L8,OR2AK2,TRIM58,OR1C1,OR5AY1
chr1 244:244.2 SMYD3
chr6 105.6:105.8 LIN28B,BVES,POPDC3,PREP
chr12 87.8:88chr17 51.4:51.6 ANKFN1
chr4 170.4:170.6 SH3RF1,NEK1
chr20 48.8:49 PARD6B,BCAS4,ADNP,DPM1,MOCS3
chr3 176.6:176.8 NAALADL2
chr8 116:116.2chr11 103.8:104chr6 128.8:129 PTPRK
chr6 4.6:4.8 KU−MEL−3,CDYL
chr9 16:16.2 C9orf93
chr5 11.6:11.8 CTNND2
chr12 125.6:125.8chr2 152.2:152.4 NEB,ARL5A,CACNB4
chr11 87:87.2chr5 24.6:24.8 CDH10
chr4 33.4:33.6chr4 14.2:14.4
BiakaPygmy
BantuEurope
Mideast
S.AsiaE.Asia
Oceania
America
0.05
0.001
Figure 24: The top 1% of XP-EHH signals in the Middle East, ordered from top to bottom in orderof significance. See the caption of Figure 1 in the main text for details.
27
chr22 45:45.2 FLJ20699,PPARA,LOC150383,PKDREJ,GTSE1,TRMU,CELSR1
chr7 119.4:119.8 KCND2
chr3 176.6:177 NAALADL2
chr21 16.8:17 C21orf34
chr15 46:46.4 SLC24A5,MYEF2,SLC12A1,DUT
chr17 60.6:60.8 RGS9
chr4 29.4:29.8chr17 56.2:56.6 BCAS3
chr12 87.4:87.8 KITLG
chr3 25.6:26 RARB,TOP2B,NGLY1,OXSM
chr16 84.4:84.6 COX4NB,COX4I1,IRF8
chr17 50.8:51.2 HLF,MMD,TMEM100,PCTP
chr20 52.4:52.6 DOK5
chr6 105.6:105.8 LIN28B,BVES,POPDC3,PREP
chr10 65.4:65.8chr15 46.6:46.8 CEP152,FBN1
chr12 2.6:2.8 FKBP4,ITFG2,NRIP2,FOXM1,CACNA1C
chr6 0:0.2 DUSP22,FLJ43763
chr4 41.8:42 SLC30A9,CCDC4
chr10 84:84.2 NRG3
chr17 52:52.2 NOG
chr9 32.6:32.8 NDUFB6,TAF1L,LOC401498
chr10 22.4:22.8 COMMD3,BMI1,SPAG6
chr10 59.2:59.4chr14 62.6:63 KCNH5,RHOJ,GPHB5,PPP2R5E
chr10 100.2:100.4 C10orf33,HPS1,HPSE2
chr12 57.6:57.8 LRIG3
chr7 118.2:118.6chr2 178:178.4 PDE11A,AGPS,TTC30A,TTC30B
chrX 110:110.4 PAK3,CAPN6,DCX
chr20 48.8:49 PARD6B,BCAS4,ADNP,DPM1,MOCS3
chr8 139.6:140 C8ORFK32,COL22A1
chr3 26.2:26.4chr12 125.6:125.8
chr3 31.2:31.6 STT3B
chr9 90.2:90.4 SPIN1,C9orf121
chr4 82.2:82.4 BMP3,PRKG2
chr22 20.6:20.8 MAPK1,PPM1F,TOP3B
chr15 27:27.4 APBA2,NDNL2
chr10 83.6:83.8 NRG3
chr4 55.8:56 SRD5A2L,TMEM165,CLOCK
chr21 16.2:16.6 USP25,C21orf34
chr7 18.6:18.8 HDAC9
chr4 5.2:5.4 STK32B
chr11 109.2:109.4chr7 118.8:119.2
chr5 109.6:110chr9 3.2:3.4 RFX3
chr11 87:87.4chr21 15.8:16 USP25
chr2 218.8:219 GPBAR1,PNKD,ARPC2,TMBIM1,MGC50811,SLC11A1,CTDSP1,VIL1,USP37,AAMP
chr7 145.4:145.8 CNTNAP2
chr6 143:143.2 HIVEP2
chr17 55.6:56 CA4,USP32,C17orf64,APPBP2,PPM1D
chr4 84.2:84.4 LIN54,COPS4,PLAC8,HPSE,COQ2
chr12 126.8:127chr1 35.6:35.8 ZMYM4,KIAA0319L,NCDN,TFAP2E,PSMB2
chr6 73.8:74 C6orf148,KCNQ5
chr2 237.6:237.8 COPS8
chr12 65.6:66 CAND1
chr5 26.4:26.6chr15 67.6:67.8chrX 111:111.2 ZCCHC16,TRPC5
chr8 11:11.2 C8orf15,MTMR9,AMAC1L2,XKR6
chr13 91.2:91.6 GPC5
chr8 37:37.2chr18 64.8:65 CCDC102B
chr15 33.6:33.8 ATPBD4
chr17 52.6:52.8 AKAP1,MSI2
chr11 129.4:129.6 PRDM10,C11orf37,APLP2,ST14,ZBTB44
chr9 107:107.2 SLC44A1
chr2 205.8:206 PARD3B
chr1 203:203.2 NFASC
chr1 36.2:36.4 EIF2C1,EIF2C3,TEKT2,ADPRHL2,COL8A2,TRAPPC3,MAP7D1
chr12 116.4:116.6 KSR2
chr2 231.4:231.6 GPR55,CAB39,ITM2C,PSMD1
chr3 142.2:142.6 SLC25A36,SPSB4,ACPL2,ZBTB38
chr17 11:11.2 FLJ45455
chr3 167:167.2 BCHE
chr10 118:118.2 GFRA1,C10orf96,PNLIPRP3
chr21 29.8:30 GRIK1
chr13 32.2:32.4 APRIN
chr4 33.4:33.6chr1 187.4:187.6chr13 103:103.2
chr3 43.2:43.4 TMEM16K,SNRK
chr10 59.6:59.8 IPMK,ZCD1,UBE2D1,TFAM
chr17 51.4:51.6 ANKFN1
chrX 110.6:110.8 ALG13
chr18 11.2:11.4chr2 192:192.2 MYO1B
BiakaPygmy
BantuEurope
Mideast
S.AsiaE.Asia
Oceania
America
0.05
0.001
Figure 25: The top 1% of XP-EHH signals in South Asia, ordered from top to bottom in order ofsignificance. See the caption of Figure 1 in the main text for details.
28
chr11 25.2:25.6
chr15 61.4:61.8 APH1B,CA12,USP3,FBXL22,HERC1
chr2 177:177.4
chr22 21.6:21.8 RTDR1,GNAZ,RAB36
chr4 158.6:159
chr22 45:45.2 FLJ20699,PPARA,LOC150383,PKDREJ,GTSE1,TRMU,CELSR1
chr17 56.2:56.6 BCAS3
chr4 5.8:6.2 EVC2,CRMP1,FLJ46481,JAKMIP1,EVC
chr8 139:139.2 C8ORFK32
chr2 9.2:9.6 ITGB1BP1,DDEF2,CPSF3,IAH1,ADAM17,YWHAQ
chr3 26.2:26.4
chr3 176.6:177 NAALADL2
chr21 16.2:16.6 USP25,C21orf34
chr2 125.4:125.8 CNTNAP5
chr2 198.6:199 PLCL1
chr2 17.8:18 SMC6,FLJ40869,KCNS3
chr2 108.8:109 RANBP2,FLJ32745,EDAR
chr16 64.2:64.6
chr4 159.2:159.4 C4orf18,TMEM144
chr20 58.2:58.4 LOC284757
chr2 17.2:17.6 VSNL1
chr10 59.2:59.4
chr8 10.8:11.2 C8orf15,MTMR9,AMAC1L2,XKR6
chr3 25.6:26 RARB,TOP2B,NGLY1,OXSM
chr1 103.2:103.6 COL11A1
chrX 110:110.4 PAK3,CAPN6,DCX
chr6 105.6:106 LIN28B,BVES,POPDC3,PREP
chr21 41.4:41.6 PLAC4,BACE2,FAM3B
chr10 94.4:94.8 KIF11,HHEX,EXOC6,CYP26C1,CYP26A1
chr17 53.2:53.6 OR4D2,MRPS23,CUEDC1,VEZF1,DYNLL2,OR4D1,EPX,MKS1,SFRS1
chr5 117.2:117.6
chr1 170.8:171.2 C1orf9,FASLG
chr7 135.4:135.6
chr2 126:126.2
chr4 41.4:41.8 DKFZP686A01247,PHOX2B,TMEM33,WDR21B,SLC30A9,CCDC4
chr1 64:64.4 ROR1,UBE2U
chr4 144.4:144.6 USP38,GAB1
chr4 7.6:7.8 AFAP1,SORCS2
chr4 143.8:144.2
chr12 125.4:125.8
chr2 108.2:108.6 SULT1C3,SULT1C1,SULT1C2,GCC2,LIMS1
chr14 68.6:68.8 WDR22,EXDL2,GALNTL1
chr4 84.2:84.4 LIN54,COPS4,PLAC8,HPSE,COQ2
chr3 108.8:109.2 BBX,CD47
chr3 44.6:45 ZNF167,ZNF660,ZNF197,ZNF35,ZNF502,ZNF501,KIAA1143,KIF15,TMEM42,TGM4,ZDHHC3,EXOSC7,CLEC3B
chr15 62:62.2 DAPK2,FAM96A,SNX1,SNX22,PPIB,CSNK1G1
chr7 112:112.4 TMEM168,FLJ31818
chr2 43.4:43.8 THADA,PLEKHH2
chr6 129.4:129.6 LAMA2
chr7 3.8:4.2 SDK1
chr10 55.6:55.8 PCDH15
chr21 16.8:17 C21orf34
chr2 212.8:213.2 ERBB4
chr4 168.8:169.2
chr4 170.8:171 NEK1,CLCN3,C4orf27
chr8 135:135.4
chrX 111:111.2 ZCCHC16,TRPC5
chr17 55.6:55.8 CA4,USP32
chr5 117.8:118
chr6 4.8:5 CDYL,RPP40
chr3 103.6:103.8 ZPLD1
chr7 29.8:30 SCRN1,FKBP14,PLEKHA8,WIPF3
chr20 30:30.4 TTLL9,PDRG1,XKR7,C20orf160,HCK,TM9SF4,PLAGL2,POFUT1,KIF3B,ASXL1
chr1 232.8:233 IRF2BP2
chr9 32.6:32.8 NDUFB6,TAF1L,LOC401498
chr6 125.8:126
chr4 191:191.2 DUX4,FRG1,TUBB4Q,DUX4C,FRG2
chr11 60.2:60.4 MS4A8B,MGC35295,MS4A10,CCDC86,GPR44,ZP1,PRPF19,TMEM109,TMEM132A
chr1 8.2:8.6 RERE,SLC45A1
chr4 28.4:28.6
chr2 25.8:26 DTNB,ASXL2,KIF3C
chr4 170.4:170.6 SH3RF1,NEK1
chr15 62.6:62.8 ZNF609,OAZ2,RBPMS2
chr9 13.8:14
chr12 87.6:87.8
chr15 44:44.2
chr12 122.6:122.8 FLJ39378,DDX55,EIF2B1,GTF2H3,C12orf38,ATP6V0A2,DNAH10,TMED2
chrX 110.6:110.8 ALG13
chr3 187.4:187.6 DGKG
BiakaPygmy
BantuEurope
Mideast
S.AsiaE.Asia
Oceania
America
0.05
0.001
Figure 26: The top 1% of XP-EHH signals in East Asia, ordered from top to bottom in order ofsignificance. See the caption of Figure 1 in the main text for details.
29
chr22 21.6:21.8 RTDR1,GNAZ,RAB36
chr2 177.8:178.2 HNRPA3,PDE11A,NFE2L2,AGPS,TTC30A,TTC30B
chr22 46.4:46.6 FLJ46257
chr2 178.4:178.8 DRB1,PDE11A,OSBPL6
chr4 158.2:158.6 GLRB,GRIA2
chr10 59.2:59.4chr12 125.4:125.8
chr4 158.8:159chr17 56.2:56.6 BCAS3
chr3 157.2:157.6 KCNAB1
chr22 45:45.2 FLJ20699,PPARA,LOC150383,PKDREJ,GTSE1,TRMU,CELSR1
chr10 115:115.4 HABP2,NRAP,CASP7
chr2 158.2:158.6 ACVR1C,ACVR1,UPP2
chr16 11:11.4 PRM1,KIAA0350,SOCS1,TNP2,PRM3,PRM2,C16orf75,LOC400499
chr19 46.6:46.8 TGFB1,MGC4093,EXOSC5,BCKDHA,B3GNT8,FLJ10241,CEACAM21,CEACAM4,TMEM91
chr5 107.2:107.6 FBXL17
chr12 1:1.4 ERC1
chr15 58.2:58.4 ANXA2
chr5 169:169.2 CCDC99,DOCK2
chr6 48.6:49chr12 30.4:30.6chr5 154.6:155chr6 49.2:49.4
chr1 165.2:165.6 C1orf32,MAEL,GPA33,POU2F1,DUSP27
chr2 108.4:108.8 SULT1C2,GCC2,LIMS1,RANBP2,FLJ32745
chr12 26:26.4 RASSF8,BHLHB3,SSPN,ITPR2
chr6 105.8:106.2 PREP
chr7 145.4:145.8 CNTNAP2
chrX 110:110.4 PAK3,CAPN6,DCX
chr15 43.8:44.2 SQRDL
chr21 14.8:15 SAMSN1
chr6 111:111.4 CDC2L6,AMD1,C6orf51,BXDC1
chr21 16.2:16.6 USP25,C21orf34
chr5 140.6:141 PCDHB9,PCDHB10,PCDHB11,PCDHB12,PCDHB13,PCDHB14,PCDHB15,SLC25A2,TAF7,PCDHGA1,PCDHGA2,PCDHGA3,PCDHGB1,PCDHGA4,PCDHGB2,PCDHGA5,PCDHGB3,PCDHGA6,PCDHGA7,PCDHGB4,PCDHGA8,PCDHGB5,PCDHGA9,PCDHGB6,PCDHGA10,PCDHGB7,PCDHGA11,PCDHGA12,PCDHGC3,PCDHGC4,PCDHGC5,HDAC3,C5orf16,FCHSD1,CENTD3,DIAPH1
chr5 153.6:153.8 GALNT10,SAP30L,HAND1
chr6 134.6:135chr20 32.6:33 ACSS2,ITCH,DYNLRB1,MAP1LC3A,PIGU,TP53INP2,NCOA6,GSS,MYH7B,GGTL3
chr1 178:178.4 C1orf76,TOR1AIP2,IFRG15,TOR1AIP1,QSCN6,CEP350
chr4 61.4:61.6chr22 39.4:39.8 MKL1,MCHR1,SLC25A17,ST13,XPNPEP3,DNAJB7,RBX1,EP300
chr10 2.8:3chr2 158.8:159.2 LOC130940,PKP4
chr6 35.2:35.4 ANKS1A,TCP11,SCUBE3,ZNF76,DEF6,PPARD
chr8 11:11.2 C8orf15,MTMR9,AMAC1L2,XKR6
chr5 108:108.2 FER
chr18 11.2:11.4chr22 40:40.2 L3MBTL2,RANGAP1,ZC3H7B,TEF,TOB2,PHF5A,ACO2
chr22 48.2:48.4 FLJ44385,C22orf34
chr5 173.2:173.4 CPEB4,HMP19
chr3 190:190.2 LPP
chr6 125.8:126chr2 3.6:3.8 RNASEH1,RPS7,COLEC11,ALLC
chr2 28.2:28.6 BRE,FOSL2,PLB1
chr10 110:110.2chr9 122.4:122.6 FBXW2,CDK5RAP2,PSMD5,MEGF9
chr6 162:162.2 PARK2
chrX 111:111.2 ZCCHC16,TRPC5
chr11 46.4:46.6 DGKZ,MDK,CHRM4,FLJ20294,C11orf77,KIAA0652
chr3 158:158.2 FLJ16641
chr5 8.6:8.8chr10 59.6:59.8 IPMK,ZCD1,UBE2D1,TFAM
chr4 60.8:61.2chr11 92.8:93 C11orf75,CCDC67
chr2 17.6:18 VSNL1,SMC6,FLJ40869,KCNS3
chr2 9.4:9.8 ITGB1BP1,DDEF2,CPSF3,IAH1,ADAM17,YWHAQ
chr4 160.6:160.8chr5 150.4:150.6 TNIP1,ANXA6,CCDC69,GM2A,SLC36A3,GPX3
chr10 22.8:23 PIP5K2A
chr1 27.6:27.8 FGR,SYTL1,MAP3K6,FCN3,GPR3,WASF2,AHDC1,CD164L2
chr6 54.6:55 FAM83B
chr22 43:43.2chr21 16.8:17 C21orf34
chr4 29.4:29.6chr13 79.4:79.6
chr7 135.4:135.6chr2 161.2:161.4
chr2 27.8:28 SLC4A1AP,RBKS,BRE,MRPL33
chr6 155.6:155.8 TIAM2,TFB1M,CLDN20,NOX3
chr12 87.6:87.8chr11 25.4:25.6
chr19 23:23.2chr3 24:24.2 NR1D2,THRB
chr2 127.8:128 ERCC3,MAP3K2,IWS1,PROC,MYO7B
chr5 134.6:134.8 H2AFY,C5orf20
BiakaPygmy
BantuEurope
Mideast
S.AsiaE.Asia
Oceania
America
0.05
0.001
Figure 27: The top 1% of XP-EHH signals in the Americas, ordered from top to bottom in orderof significance. See the caption of Figure 1 in the main text for details.
30
chr22 44.8:45.2 FLJ20699,WNT7B,FLJ27365,PPARA,LOC150383,PKDREJ,GTSE1,TRMU,CELSR1,C22orf26
chr6 105.2:105.6 HACE1,LIN28B
chr12 65.6:66 CAND1
chr21 16.2:16.6 USP25,C21orf34
chr4 95:95.4 ATOH1,SMARCAD1,PGDS
chr8 100:100.4 OSR2,VPS13B
chr8 19.4:19.8 ChGn,INTS10,LPL
chr9 38:38.4 SHB,ALDH1B1,IGFBPL1
chr1 174.8:175.2 ASTN1,PAPPA2
chr5 58.6:59 PDE4D
chr8 134.8:135.2
chr6 105.8:106 PREP
chr4 170.8:171.2 NEK1,CLCN3,C4orf27,MFAP3L,AADAT
chr4 170.2:170.6 CBR4,SH3RF1,NEK1
chr1 113.2:113.6 LRIG2,SLC16A1
chr2 22.2:22.6
chr20 5.8:6 C20orf196,CHGB,CGI−09,MCM8,CRLS1,C20orf75,C20orf42
chr4 55.8:56.2 SRD5A2L,TMEM165,CLOCK,PDCL2,NMU
chr5 59.8:60.2 DEPDC1B,ELOVL7,ERCC8
chr22 24.8:25 MYO18B,SEZ6L
chr4 85.2:85.6 NKX6−1
chrX 110:110.4 PAK3,CAPN6,DCX
chr4 95.6:95.8 PDLIM5
chr2 237:237.4 CXCR7,IQCA
chr11 120.6:121 TECTA,SORL1,SC5DL
chr2 20.2:20.6 SDC1,PUM2,RHOB
chr5 59.2:59.6
chr12 116.4:116.6 KSR2
chr21 17.6:17.8 CXADR
chr4 159.6:159.8 RXFP1,LOC201725,PPID,ETFDH
chr11 25.2:25.6
chr11 30.8:31.2 DCDC5,DCDC1
chr2 165.8:166.2 SCN2A,SCN3A,FAM130A2
chr11 31.4:31.8 DPH4,IMMP1L,PAX6,ELP4
chr12 92.8:93 CRADD
chr2 212.8:213.2 ERBB4
chr8 63.6:64 FAM77D
chr4 160:160.4 FLJ25371
chr2 2.8:3.2 TSSC1
chr3 71.4:71.8 FOXP1,EIF4E3
chr17 50.8:51 HLF,MMD
chr2 142.6:143 LRP1B
chr18 11.6:11.8 GNAL,CHMP1B
chr22 40.4:40.6 MEI1,XRCC6,NHP2L1,FLJ23584,CCDC134,SREBF2
chr4 186.6:186.8 ANKRD37,C4orf20,CCDC110,PDLIM3,SORBS2
chr7 29.8:30 SCRN1,FKBP14,PLEKHA8,WIPF3
chrX 111:111.2 ZCCHC16,TRPC5
chr8 11:11.2 C8orf15,MTMR9,AMAC1L2,XKR6
chr8 100.6:100.8 VPS13B
chr9 0.8:1 DMRT1,DMRT3,DMRT2
chr10 65.6:66
chr16 60:60.2 CDH8
chr5 30.6:30.8
chr13 110.4:110.8 ANKRD10,ARHGEF7,C13orf16
chr7 142:142.2 PRSS1,PRSS2
chr5 170.2:170.6 GABRP,RANBP17
chr10 6.8:7.2 SFMBT2
chr16 5.4:5.6
chr2 205.8:206 PARD3B
chr16 77.2:77.4 WWOX
chr11 44:44.2 LOC390110,PHACS,EXT2,ALX4
chr18 11.2:11.4
chr3 179.2:179.4
chr2 64.2:64.4 PELI1
chr8 99.6:99.8 STK3
chr22 39.8:40.2 EP300,L3MBTL2,RANGAP1,ZC3H7B,TEF,TOB2,PHF5A,ACO2
chr2 126:126.2
chr21 16.8:17 C21orf34
chr1 203.4:203.8 RBBP5,RIPK5,TMCC2,NUAK2,KLHDC8A,LEMD1,PCTK3,MFSD4
chr13 43.6:43.8 C13orf21
chr8 64.6:64.8
chrX 110.6:110.8 ALG13
chr10 9:9.2
chr5 99.4:99.6
chr2 232.2:232.4 MGC35154,PTMA,PDE6D,COPS7B
chr20 0:0.2 DEFB125,DEFB126,DEFB127,DEFB128,DEFB129,DEFB32,C20orf96,ZCCHC3
BiakaPygmy
BantuEurope
Mideast
S.AsiaE.Asia
Oceania
America
0.05
0.001
Figure 28: The top 1% of XP-EHH signals in Oceania, ordered from top to bottom in order ofsignificance. See the caption of Figure 1 in the main text for details.
31
References
[1] Clark AG, Hubisz MJ, Bustamante CD, Williamson SH, Nielsen R (2005) Ascertainment biasin studies of human genome-wide polymorphism. Genome Res 15: 1496–1502.
[2] Sabeti PC, Varilly P, Fry B, Lohmueller J, Hostetter E, et al. (2007) Genome-wide detectionand characterization of positive selection in human populations. Nature 449: 913–918.
[3] Schaffner SF, Foo C, Gabriel S, Reich D, Daly MJ, et al. (2005) Calibrating a coalescentsimulation of human genome sequence variation. Genome Res 15: 1576–1583.
[4] Tang K, Thornton K, Stoneking M (2007) A New Approach for Using Genome Scans to DetectRecent Positive Selection in the Human Genome. PLoS Biol 5: e171.
[5] Teshima KM, Coop G, Przeworski M (2006) How reliable are empirical genomic scans forselective sweeps? Genome Res 16: 702–712.
[6] Thornton KR, Jensen JD (2007) Controlling the false-positive rate in multilocus genome scansfor selection. Genetics 175: 737–750.
[7] Voight BF, Kudaravalli S, Wen X, Pritchard JK (2006) A map of recent positive selection inthe human genome. PLoS Biol 4: e72.
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