Selection for height genes?

Three papers on genome wide association studies & height. Identification of ten loci associated with height highlights new biological pathways in human growth, Genome-wide association analysis identifies 20 loci that influence adult height and Many sequence variants affecting diversity of adult human height. Dan MacArthur hits the major point:

ScienceDaily puts a positive spin on the story ("Scientists are beginning to develop a clearer picture of what makes some people stand head and shoulders above the rest"), but the real story is this: despite the massive scale of these studies, they're still only capturing less than 5% of the total variance in a trait that is almost entirely (90%) genetic. This is a powerful demonstration of the inability of current GWAS technology to access the genetic variants responsible for the vast majority of heritable variation in at least some complex traits, for reasons I have previously discussed in detail.

I was wondering if there was any recent selection in the genomic regions pinpointed in the three papers, so I turned to Haplotter. Below the fold are the results....

I set Haplotter so that it looked around a 1 MB window fixed on the gene I queried. X = a hit within that window, while XX = a hit on that specific gene. The columns are pretty self-explanatory, but do note some of these genes are very close to each other. Also, I had to use aliases, and I can't guarantee that a gene isn't listed twice because of the usage of aliases. All in all, note much selection, huh? I wasn't expecting much, but nice to confirm expectations....


.

Gene
Northern European
West African
East Asian
Note

.

ACAN
-
-
-
Alias: CSPG1

.

ADAMTS17
-
-
-

.

ADAMTSL3
-
-
-

.

ANAPC13
-
-
-

.

ANKFN1
-
-
-
Alias: FLJ38335

.

ANKS1
X
-
-

.

ATAD5
-
-
-
Alias: FLJ12735

.

ATXN3
-
-
-

.

BCAS3
-
-
-
Fst - No diff. Euro-Asian in some regions

.

BMP2
-
-
-

.

BMP6
-
-
-

.

C18orf45
-
-
-

.

C1orf19
-
-
-

.

C20orf30
-
-
-

.

C6orf106
XX
-
-

.

CABLES1
-
-
-

.

CDK6
-
-
-

.

CENTA2
-
-
-
Fst - No diff. Euro-Asian in some regions

.

CEP63
-
-
-

.

CHCHD7
-
-
-

.

COIL
-
-
-

.

CPSF2
-
-
-

.

CRLF3
-
-
-
Fst - No diff. Euro-Asian in some regions

.

DCC
-
-
-

.

DEF6
-
-
-
Alias: DEFA6

.

DGKE
-
-
-

.

DLEU7
-
-
-

.

DNM3
-
-
-

.

DOT1L
-
-
-

.

DYM
-
-
-

.

E4F1
-
-
-
Lots of stuff just below p-value in region

.

EFEMP1
-
-
-

.

ERVWE1
-
-
-
Problem with haplotter

.

FBLN5
-
-
-

.

FUBP3
-
-
-

.

GATAD1
-
-
-

.

GDF5
X
X
XX
Massive selection in this genomic region in Euro & Asian

.

GLT25D2
-
-
-
p-value close in Asian

.

GNA12
-
-
-

.

GPR126
-
-
-

.

GRB10
-
-
-

.

HHIP
-
-
-

.

HIST1H1D
-
-
-
Alias: H1F3, lots of close p-values

.

HMGA1
X
-
-
Signal from other gene on list

.

HMGA2
-
-

.

IHH
-
-
-
p-value close in Euro

.

LBH
-
-
-

.

LCORL
-
-
-
Alias: FLJ30696

.

LIN28B
-
-
-
p-values close for Euro

.

LOC387103
-
-
-
Alias: CUG2, haplotter

.

LYAR
-
-
-

.

LYN
-
-
-
Asians fixed, so haplotter can't detect

.

MOS
-
-
-
Alias: MSV

.

MTMR11
-
-
-
Looks like lots of fixed stuff around....

.

NACA2
-
-
-

.

NCAPG
-
-
-
Alias: CAPG

.

NKX2-1
-
-
-

.

NOG
-
-
-

.

PAPPA
-
-
-

.

PENK
-
-
-
Asians look fixed

.

PEX1
-
-
-

.

PLAG1
-
-
-

.

PNPT1
-
-
-

.

PRKG2
XX
-
-
X as well

.

PTCH1
-
-
-
Haplotter error

.

PXMP3
-
-
-

.

RAB40C
-
-
-

.

RBBP8
-
-
-
Africans look fixed

.

RDHE2
-
-
-

.

RISK
-
-
-
Can't find this gene?

.

RNF135
-
-
-
p-value close for African, looks near fixed

.

RPS20
-
-
-
Fixed in Asians?

.

SCMH1
-
-
-
Fixed in Africans?

.

SCUBE3
X
-
-

.

SF3B4
-
-
-

.

SH3GL3
-
-
-

.

SOCS2
-
-
-

.

SPAG17
-
-
-
Haplotter error

.

SV2A
-
-
-
Asians look fixed?

.

TBX2
-
-
-

.

TBX4
-
-
-

.

TCP11
X
-
-
Overlap with SCUBE3

.

TGS1
-
-
-

.

TMED3
-
-
-

.

TRIM25
-
-
-

.

TRIP11
-
-
-

.

UQCC
X
X
XX
Lots of selection in region! Alias: BFZB

.

WDR60
-
-
-

.

ZBTB38
-
-
-

.

ZFHX4
-
-
-

.

ZNF462
-
-
-

.

ZNF678
-
-
-

.

ZNF76
X
-
-
Region overlaps with others, SCUBE3
Tags

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Difference in height is 90% heritable among whom? That stat is meaningless without the group it refers to, right?

That 5% of variance explaining something that is 90% genetic is a real killer for these papers, as soon as he read that on his blog my perception of the studies was really different.

Two more years of Decode putting out these papers then we shall see no more from them :(

Difference in height is 90% heritable among whom? That stat is meaningless without the group it refers to, right?

first world populations. i see a number closer to 80% usually, but i haven't kept track of the lit.