Variant report

Variant	rs4580515
Chromosome Location	chr3:113255143-113255144
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:113254497..113255223-chr3:113296850..113297376,2	MCF-7	breast:
2	chr3:113215914..113218639-chr3:113252642..113255587,3	MCF-7	breast:
3	chr3:113254930..113255834-chr3:113270582..113271304,2	MCF-7	breast:
4	chr3:113254346..113256305-chr3:113270288..113271550,7	MCF-7	breast:
5	chr3:113229615..113239929-chr3:113247196..113257849,45	MCF-7	breast:
6	chr3:113254658..113255498-chr3:113275897..113276863,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163611	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs11914782	0.91[GIH][hapmap];0.81[JPT][hapmap]
rs11919031	0.91[GIH][hapmap];0.81[JPT][hapmap]
rs11922598	0.90[CEU][hapmap];0.82[MEX][hapmap]
rs11924017	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11929418	0.81[JPT][hapmap]
rs12695292	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1463641	0.91[GIH][hapmap];0.81[JPT][hapmap]
rs16845107	0.91[GIH][hapmap]
rs16861025	0.84[JPT][hapmap]
rs16861032	0.84[JPT][hapmap]
rs16861130	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16861157	0.86[JPT][hapmap];1.00[ASN][1000 genomes]
rs16861165	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs2007579	0.91[ASN][1000 genomes]
rs2254267	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2399483	0.91[ASN][1000 genomes]
rs2399486	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2895414	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3732799	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3732807	0.91[GIH][hapmap];0.81[JPT][hapmap]
rs3732808	0.91[GIH][hapmap];0.81[JPT][hapmap]
rs4331647	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4508746	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4621301	0.92[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58686141	0.91[ASN][1000 genomes]
rs58884094	0.96[ASN][1000 genomes]
rs59631554	0.96[ASN][1000 genomes]
rs59666592	0.91[ASN][1000 genomes]
rs6764524	0.81[JPT][hapmap]
rs6766534	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6769995	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6771864	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6776729	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6776974	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs6780755	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[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];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6782784	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6790846	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6805231	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6807610	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72946779	0.91[ASN][1000 genomes]
rs72950827	0.96[ASN][1000 genomes]
rs7612047	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7614678	0.81[JPT][hapmap]
rs7620700	0.89[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];0.96[ASN][1000 genomes]
rs7623213	0.85[JPT][hapmap]
rs7636912	0.81[JPT][hapmap]
rs7636986	0.91[GIH][hapmap];0.81[JPT][hapmap]
rs7646262	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[ASN][1000 genomes]
rs7650500	0.91[GIH][hapmap];0.81[JPT][hapmap]
rs7653791	1.00[ASN][1000 genomes]
rs9682108	0.91[ASN][1000 genomes]
rs9848190	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9852064	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9854538	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[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	nsv1013506	chr3:112890608-113680951	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv1004000	chr3:113116778-113513899	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv877349	chr3:113208224-113323787	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
4	nsv877350	chr3:113208224-113332235	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:113252600-113256400	Weak transcription	Esophagus	oesophagus
2	chr3:113253400-113256000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr3:113253600-113255400	Weak transcription	Small Intestine	intestine
4	chr3:113253800-113255600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
5	chr3:113253800-113257200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
6	chr3:113253800-113257200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr3:113253800-113257200	Enhancers	Primary T killer memory cells from peripheral blood	blood
8	chr3:113253800-113257400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr3:113253800-113260800	Weak transcription	Thymus	Thymus
10	chr3:113254000-113256200	Enhancers	Primary T helper naive cells from peripheral blood	blood
11	chr3:113254000-113256200	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr3:113254000-113257200	Enhancers	Rectal Mucosa Donor 31	rectum
13	chr3:113254000-113257800	Weak transcription	Spleen	Spleen
14	chr3:113254000-113258400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
15	chr3:113254200-113260000	Weak transcription	Fetal Thymus	thymus
16	chr3:113254400-113255200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr3:113254400-113256600	Genic enhancers	Primary T cells from cord blood	blood
18	chr3:113254400-113256800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr3:113254400-113258400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
20	chr3:113254600-113255600	Enhancers	Sigmoid Colon	Sigmoid Colon
21	chr3:113254600-113255600	Enhancers	Dnd41	blood
22	chr3:113254600-113255800	Genic enhancers	Primary T cells fromperipheralblood	blood
23	chr3:113254600-113256200	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
24	chr3:113254600-113256400	Genic enhancers	Primary B cells from peripheral blood	blood
25	chr3:113254600-113257200	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
26	chr3:113254800-113255400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
27	chr3:113254800-113257000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
28	chr3:113254800-113257200	Strong transcription	Primary B cells from cord blood	blood
29	chr3:113255000-113255200	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr3:113255000-113255200	Enhancers	Pancreatic Islets	Pancreatic Islet
31	chr3:113255000-113255200	Enhancers	Gastric	stomach
32	chr3:113255000-113255400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
33	chr3:113255000-113255400	Flanking Active TSS	A549	lung
34	chr3:113255000-113255800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
35	chr3:113255000-113256000	Enhancers	NHEK	skin
36	chr3:113255000-113256400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr3:113255000-113256400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr3:113255000-113256400	Enhancers	Hela-S3	cervix
39	chr3:113255000-113256600	Enhancers	Primary hematopoietic stem cells	blood
40	chr3:113255000-113256600	Enhancers	HMEC	breast
41	chr3:113255000-113256800	Enhancers	Primary hematopoietic stem cells short term culture	blood
42	chr3:113255000-113256800	Enhancers	Stomach Mucosa	stomach

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