Variant report

Variant	rs11171891
Chromosome Location	chr12:39764996-39764997
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:39755090..39757754-chr12:39764621..39766612,2	MCF-7	breast:
2	chr12:39764517..39769063-chr12:39834166..39838574,6	K562	blood:

Variant related genes	Relation type
ENSG00000139116	Chromatin interaction
ENSG00000252974	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10876868	0.88[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.94[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10876876	0.88[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10876886	0.87[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10876972	0.84[CEU][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap]
rs11171674	0.94[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.92[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11171675	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]
rs11171676	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11171720	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11171730	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11171789	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11171901	0.88[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.92[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11171923	0.84[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11171938	0.95[CEU][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172108	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs11172120	0.84[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap]
rs11172183	0.95[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs11172282	0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs11172492	0.84[CEU][hapmap];0.95[JPT][hapmap]
rs11172592	0.94[JPT][hapmap]
rs11830643	0.87[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11836755	0.95[CHB][hapmap];0.89[JPT][hapmap];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12228767	0.87[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12230604	0.88[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.92[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12424345	0.84[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1512936	0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1512942	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1567739	0.84[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17127019	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1828653	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.92[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1955314	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2388320	0.84[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.82[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3736466	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4284427	0.88[JPT][hapmap]
rs4320988	0.84[CEU][hapmap];0.95[JPT][hapmap]
rs4492858	0.84[CEU][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap]
rs4500523	0.82[GIH][hapmap];0.95[JPT][hapmap]
rs57756176	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57833783	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59695906	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs60792848	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7137143	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7316073	0.90[JPT][hapmap]
rs7953548	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7962283	0.83[CEU][hapmap]
rs7964447	0.87[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7968837	0.84[CEU][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap]
rs7971515	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7974928	0.91[CEU][hapmap];0.81[CHB][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap]
rs7979329	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7979444	0.82[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.93[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.85[ASN][1000 genomes]
rs958914	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
rs11171891	KIF21A	cis	cerebellum	SCAN
rs11171891	KIF21A	cis	multi-tissue	Pritchard

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:39697800-39771800	Weak transcription	Fetal Kidney	kidney
2	chr12:39721000-39770600	Weak transcription	Gastric	stomach
3	chr12:39722800-39767200	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr12:39726400-39766600	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr12:39726600-39766600	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr12:39726600-39766600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr12:39726600-39766800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr12:39726800-39766600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr12:39727000-39767000	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr12:39727000-39779200	Weak transcription	Aorta	Aorta
11	chr12:39735600-39766600	Weak transcription	HMEC	breast
12	chr12:39735600-39766600	Weak transcription	NHEK	skin
13	chr12:39737400-39766600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr12:39743000-39766800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr12:39743200-39765800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr12:39745000-39778600	Weak transcription	Pancreas	Pancrea
17	chr12:39748400-39765800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr12:39750200-39765400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr12:39751400-39770400	Weak transcription	Brain Hippocampus Middle	brain
20	chr12:39751600-39771800	Weak transcription	Brain Anterior Caudate	brain
21	chr12:39752000-39765400	Weak transcription	Left Ventricle	heart
22	chr12:39752200-39765400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr12:39752200-39766400	Weak transcription	Fetal Heart	heart
24	chr12:39752200-39767600	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr12:39752200-39769000	Weak transcription	Ovary	ovary
26	chr12:39752200-39769200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr12:39756200-39766600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr12:39756200-39767600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr12:39757000-39766600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr12:39757000-39784600	Weak transcription	Brain Germinal Matrix	brain
31	chr12:39758400-39766600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr12:39758600-39770600	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr12:39759200-39765400	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr12:39760400-39766200	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr12:39761000-39766200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr12:39761200-39766600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr12:39761200-39766800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr12:39761200-39769000	Weak transcription	Duodenum Mucosa	Duodenum
39	chr12:39761600-39766600	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr12:39761800-39806000	Weak transcription	Hela-S3	cervix
41	chr12:39762200-39766600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr12:39762600-39766400	Weak transcription	HepG2	liver
43	chr12:39762600-39766800	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr12:39762800-39765400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr12:39762800-39771200	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr12:39763000-39766000	Weak transcription	Liver	Liver
47	chr12:39763000-39766400	Weak transcription	K562	blood
48	chr12:39763000-39781400	Weak transcription	A549	lung
49	chr12:39763800-39768400	Weak transcription	Fetal Brain Female	brain
50	chr12:39764000-39766800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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