Variant report

Variant	rs10865954
Chromosome Location	chr3:49211989-49211990
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	REST	chr3:49210427-49211993	H1-neurons	neurons:	n/a	n/a
2	MXI1	chr3:49208067-49212337	SK-N-SH	brain:	n/a	chr3:49211019-49211034 chr3:49211021-49211036
3	CTCF	chr3:49211880-49212030	NB4	blood:	n/a	chr3:49211980-49211996 chr3:49211974-49211995 chr3:49211979-49211997 chr3:49211985-49211994
4	BCL3	chr3:49211930-49212200	GM12878	blood:	n/a	n/a
5	CTCF	chr3:49211880-49212030	HRPEpiC	eye:	n/a	chr3:49211980-49211996 chr3:49211974-49211995 chr3:49211979-49211997 chr3:49211985-49211994
6	CTCF	chr3:49211900-49212050	HRPEpiC	eye:	n/a	chr3:49211980-49211996 chr3:49211974-49211995 chr3:49211979-49211997 chr3:49211985-49211994

No.	Distal block	Cell Line	Cell type
1	chr3:49141299..49143181-chr3:49211040..49212899,2	K562	blood:
2	chr3:49207667..49210496-chr3:49210545..49213014,4	K562	blood:
3	chr3:49207629..49210061-chr3:49211282..49215140,3	MCF-7	breast:
4	chr3:49198168..49200645-chr3:49211215..49212732,2	K562	blood:
5	chr3:49195402..49201533-chr3:49207296..49212401,9	MCF-7	breast:

Variant related genes	Relation type
KLHDC8B	TF binding region
ENSG00000185909	Chromatin interaction
ENSG00000172053	Chromatin interaction
ENSG00000270441	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 25 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10049462	1.00[JPT][hapmap]
rs10154895	0.89[ASN][1000 genomes]
rs11130182	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11130184	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1134043	0.96[LWK][hapmap];0.90[MKK][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes]
rs11552724	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11706052	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs11706189	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11712006	0.85[ASN][1000 genomes]
rs11713297	0.87[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11715581	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11716334	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11717524	0.80[EUR][1000 genomes]
rs11719220	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs11920267	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12487580	0.90[ASN][1000 genomes]
rs12490393	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12493001	0.87[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap];0.89[ASN][1000 genomes]
rs12629759	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.82[YRI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12631989	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap]
rs12636030	0.89[ASN][1000 genomes]
rs12637576	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13064784	0.90[ASN][1000 genomes]
rs13068038	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs13077498	1.00[JPT][hapmap]
rs13096406	0.81[ASN][1000 genomes]
rs2117938	0.89[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2304442	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2334958	0.82[EUR][1000 genomes]
rs3212	0.82[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.90[ASN][1000 genomes]
rs34326553	0.85[ASN][1000 genomes]
rs34566463	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs34580506	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs34889065	0.85[ASN][1000 genomes]
rs35060561	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs35174559	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes]
rs35283189	0.87[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs35673421	0.87[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs36133651	0.86[AFR][1000 genomes]
rs3774800	1.00[GIH][hapmap];0.90[TSI][hapmap]
rs4279134	0.84[ASW][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.90[ASN][1000 genomes]
rs4308307	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4367098	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4499638	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4513485	0.94[ASW][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.83[MEX][hapmap];0.86[MKK][hapmap];0.88[TSI][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs4521268	0.82[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.90[ASN][1000 genomes]
rs4536858	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4955410	0.94[ASW][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.82[MEX][hapmap];0.81[MKK][hapmap];0.88[TSI][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs4955418	1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4955419	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4955420	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4955432	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs4974080	0.82[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs5030795	0.87[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs55713230	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61583136	0.95[ASN][1000 genomes]
rs62262517	0.88[ASN][1000 genomes]
rs6414613	0.84[ASW][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs6446205	0.82[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs66991555	0.95[ASN][1000 genomes]
rs6770112	0.95[ASN][1000 genomes]
rs6772452	0.84[ASW][hapmap]
rs6779394	1.00[JPT][hapmap];0.88[TSI][hapmap];0.85[ASN][1000 genomes]
rs6781790	0.82[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs6784111	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6790914	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6794924	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6795756	0.83[EUR][1000 genomes]
rs7432989	0.87[CHD][hapmap];0.85[TSI][hapmap]
rs7615235	0.87[ASN][1000 genomes]
rs7621015	0.82[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap]
rs7626445	0.82[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.90[ASN][1000 genomes]
rs7632267	0.83[AFR][1000 genomes]
rs7652746	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9311439	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9814987	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs9835439	0.89[ASN][1000 genomes]
rs9837237	0.87[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9837625	0.87[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9840050	0.82[CHB][hapmap];0.87[CHD][hapmap];0.85[TSI][hapmap];0.90[ASN][1000 genomes]
rs9846123	0.84[ASW][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs9847839	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs9850917	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9855123	0.89[ASN][1000 genomes]
rs9862483	0.89[ASN][1000 genomes]
rs9880088	0.87[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs9880309	1.00[JPT][hapmap]
rs9990153	0.87[CHD][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876764	chr3:49040462-49245645	Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	279 gene(s)	inside rSNPs	diseases
2	nsv834686	chr3:49106047-49270556	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
3	nsv1008750	chr3:49208815-49362401	Weak transcription Genic enhancers Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:25)

SNP	Gene	Cis/trans	Tissue	Source
rs10865954	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs10865954	WDR6	cis	Esophagus Mucosa	GTEx
rs10865954	WDR6	cis	parietal	SCAN
rs10865954	CCDC36	cis	lung	GTEx
rs10865954	WDR6	cis	Nerve Tibial	GTEx
rs10865954	C3orf62	cis	cerebellum	SCAN
rs10865954	WDR6	cis	lymphoblastoid	seeQTL
rs10865954	P4HTM	cis	parietal	SCAN
rs10865954	CCDC36	cis	Artery Tibial	GTEx
rs10865954	WDR6	cis	Adipose Subcutaneous	GTEx
rs10865954	AMT	cis	parietal	SCAN
rs10865954	PH-4	Cis_1M	lymphoblastoid	RTeQTL
rs10865954	WDR6	cis	Whole Blood	GTEx
rs10865954	TLR9	cis	parietal	SCAN
rs10865954	WDR6	cis	Heart Left Ventricle	GTEx
rs10865954	CCDC36	cis	Esophagus Muscularis	GTEx
rs10865954	AMT	cis	Thyroid	GTEx
rs10865954	DALRD3	cis	cerebellum	SCAN
rs10865954	WDR6	cis	Muscle Skeletal	GTEx
rs10865954	WDR6	cis	cerebellum	SCAN
rs10865954	CCDC71	cis	cerebellum	SCAN
rs10865954	WDR6	cis	Artery Tibial	GTEx
rs10865954	WDR6	cis	lung	GTEx
rs10865954	SEMA3G	cis	cerebellum	SCAN
rs10865954	AMT	cis	cerebellum	SCAN

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49208200-49212000	Flanking Active TSS	Brain Germinal Matrix	brain
2	chr3:49209200-49212000	Flanking Active TSS	Fetal Brain Female	brain
3	chr3:49209200-49212400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr3:49209600-49212000	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr3:49209600-49212000	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
6	chr3:49209600-49213800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr3:49209800-49212000	Enhancers	H1 Cell Line	embryonic stem cell
8	chr3:49209800-49212400	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr3:49209800-49212600	Enhancers	Fetal Brain Male	brain
10	chr3:49209800-49215000	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr3:49210000-49212000	Enhancers	Osteobl	bone
12	chr3:49210000-49212800	Transcr. at gene 5' and 3'	Fetal Adrenal Gland	Adrenal Gland
13	chr3:49210000-49213000	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr3:49210200-49212000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr3:49210400-49212400	Enhancers	NH-A	brain
16	chr3:49210400-49212800	Weak transcription	Aorta	Aorta
17	chr3:49210400-49213800	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr3:49210600-49212000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr3:49210600-49212000	Enhancers	Gastric	stomach
20	chr3:49210600-49212200	Enhancers	Brain Cingulate Gyrus	brain
21	chr3:49210800-49212000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr3:49210800-49212200	Enhancers	Brain Anterior Caudate	brain
23	chr3:49210800-49212800	Genic enhancers	Fetal Stomach	stomach
24	chr3:49210800-49214600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr3:49211000-49212000	Enhancers	Brain Angular Gyrus	brain
26	chr3:49211000-49212600	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr3:49211000-49215200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr3:49211200-49212000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr3:49211200-49212000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr3:49211200-49212000	Enhancers	Colonic Mucosa	Colon
31	chr3:49211200-49212200	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr3:49211200-49212200	Flanking Active TSS	Fetal Heart	heart
33	chr3:49211200-49213800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr3:49211200-49214200	Weak transcription	A549	lung
35	chr3:49211200-49214600	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr3:49211200-49218800	Weak transcription	Fetal Kidney	kidney
37	chr3:49211200-49224600	Weak transcription	Primary hematopoietic stem cells	blood
38	chr3:49211400-49212000	Enhancers	iPS-15b Cell Line	embryonic stem cell
39	chr3:49211400-49212000	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr3:49211400-49212000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr3:49211400-49212000	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr3:49211400-49212000	Transcr. at gene 5' and 3'	Colon Smooth Muscle	Colon
43	chr3:49211400-49212000	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
44	chr3:49211400-49212000	Genic enhancers	HSMM	muscle
45	chr3:49211400-49212800	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr3:49211400-49212800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr3:49211400-49213800	Weak transcription	HUVEC	blood vessel
48	chr3:49211400-49214400	Weak transcription	Duodenum Mucosa	Duodenum
49	chr3:49211400-49214400	Genic enhancers	Left Ventricle	heart
50	chr3:49211400-49215000	Weak transcription	NHDF-Ad	bronchial

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