Variant report

Variant	rs11171675
Chromosome Location	chr12:39687989-39687990
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10876868	0.94[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.98[LWK][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10876876	0.94[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10876886	0.87[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10876972	0.83[CEU][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.82[TSI][hapmap]
rs11171674	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11171676	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11171720	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11171730	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11171789	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.98[LWK][hapmap];0.84[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11171891	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.95[LWK][hapmap];0.84[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11171901	0.94[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11171923	0.83[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11171938	0.95[CEU][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11172108	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs11172120	0.83[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap]
rs11172183	0.95[CEU][hapmap];0.84[CHB][hapmap];0.94[JPT][hapmap];0.84[YRI][hapmap]
rs11172282	0.95[CEU][hapmap];0.82[CHB][hapmap];0.94[JPT][hapmap];0.92[YRI][hapmap]
rs11830643	0.87[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11836755	0.95[CHB][hapmap];0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs12228767	0.87[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12230604	0.94[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12424345	0.83[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1512936	0.95[CHB][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1512942	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1567739	0.83[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17127019	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1828653	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1955314	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2388320	0.83[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.82[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3736466	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4492858	0.83[CEU][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.82[TSI][hapmap]
rs57756176	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57833783	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60792848	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7137143	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.95[LWK][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7953548	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7962283	0.82[CEU][hapmap]
rs7964447	0.87[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7971515	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7974928	0.91[CEU][hapmap];0.81[CHB][hapmap];0.91[GIH][hapmap];0.84[MEX][hapmap];0.91[TSI][hapmap]
rs7979329	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7979444	0.88[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.82[ASN][1000 genomes]
rs958914	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899013	chr12:39567945-39732430	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	nsv832375	chr12:39599362-39784722	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv832376	chr12:39633080-39808277	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv470286	chr12:39651893-39729700	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv558589	chr12:39667861-39768356	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
6	nsv531527	chr12:39680812-40182822	Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11171675	KIF21A	cis	multi-tissue	Pritchard
rs11171675	KIF21A	cis	cerebellum	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:39674800-39690200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr12:39682000-39699200	Weak transcription	Hela-S3	cervix
3	chr12:39682400-39688800	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr12:39683200-39696000	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr12:39684400-39695400	Weak transcription	A549	lung
6	chr12:39684600-39688000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr12:39684600-39688200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr12:39685200-39697400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr12:39685200-39714400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr12:39685600-39688800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr12:39686000-39688200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr12:39686400-39699600	Weak transcription	HMEC	breast
13	chr12:39686600-39688000	Weak transcription	Brain Germinal Matrix	brain
14	chr12:39686600-39688400	Weak transcription	Fetal Brain Male	brain
15	chr12:39686600-39722400	Weak transcription	GM12878-XiMat	blood
16	chr12:39686600-39725400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr12:39686800-39729800	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr12:39686800-39738800	Weak transcription	Pancreas	Pancrea
19	chr12:39687200-39696800	Weak transcription	Stomach Smooth Muscle	stomach
20	chr12:39687200-39726400	Weak transcription	Fetal Intestine Small	intestine
21	chr12:39687600-39688800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr12:39687600-39723800	Weak transcription	Duodenum Mucosa	Duodenum
23	chr12:39687800-39688200	Enhancers	Brain Anterior Caudate	brain

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