Variant report

Variant	rs6580768
Chromosome Location	chr12:51172739-51172740
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:51155325..51162343-chr12:51172009..51182370,14	MCF-7	breast:
2	chr12:51169144..51170647-chr12:51172407..51174153,2	MCF-7	breast:
3	chr12:51156141..51159167-chr12:51172067..51175180,3	MCF-7	breast:
4	chr12:51171915..51173515-chr12:51175788..51178254,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000123268	Chromatin interaction

Extended variants
information (count: 94 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10506296	1.00[CEU][hapmap];0.89[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10735827	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10747590	0.89[ASN][1000 genomes]
rs10747592	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10747593	0.95[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10783368	0.90[EUR][1000 genomes]
rs10783388	0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10783390	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap]
rs10876048	0.90[EUR][1000 genomes]
rs10876054	0.90[EUR][1000 genomes]
rs10876057	0.82[EUR][1000 genomes]
rs10876082	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10876083	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10876085	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10876088	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10876091	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11169551	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11169553	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11169556	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12099615	0.86[EUR][1000 genomes]
rs12296379	0.86[EUR][1000 genomes]
rs12320201	0.90[EUR][1000 genomes]
rs1402693	1.00[CEU][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs1521515	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1521517	1.00[CEU][hapmap];0.89[CHB][hapmap];0.83[CHD][hapmap];0.87[JPT][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs1561422	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs17124888	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs17124907	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1815010	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1996750	0.86[EUR][1000 genomes]
rs2246840	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2252595	1.00[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes]
rs2684886	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2684890	1.00[CEU][hapmap];0.89[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2684891	1.00[CEU][hapmap];0.89[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2684902	1.00[CEU][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs2684906	1.00[CEU][hapmap];0.89[CHB][hapmap];0.87[JPT][hapmap];0.90[EUR][1000 genomes]
rs2700486	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28414775	0.86[EUR][1000 genomes]
rs2947617	0.90[EUR][1000 genomes]
rs3803181	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3825401	1.00[CEU][hapmap];0.89[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4129355	0.90[EUR][1000 genomes]
rs4143663	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4562889	1.00[CEU][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap]
rs4768862	0.91[ASN][1000 genomes]
rs4768887	0.90[EUR][1000 genomes]
rs4768909	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4768915	0.85[CHB][hapmap];0.95[JPT][hapmap];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4768920	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56753963	0.86[EUR][1000 genomes]
rs56818625	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57328764	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57512759	0.86[EUR][1000 genomes]
rs58301497	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs58943330	0.86[EUR][1000 genomes]
rs59194948	0.86[EUR][1000 genomes]
rs59284993	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59683461	0.86[EUR][1000 genomes]
rs60239257	0.86[EUR][1000 genomes]
rs60494920	0.86[EUR][1000 genomes]
rs60908906	0.86[EUR][1000 genomes]
rs61926300	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6580766	1.00[CEU][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6580767	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[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]
rs6580770	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7132443	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7135222	0.90[EUR][1000 genomes]
rs7301125	0.90[EUR][1000 genomes]
rs7303202	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7304793	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7306387	0.86[EUR][1000 genomes]
rs7308872	0.85[ASN][1000 genomes]
rs7310507	0.86[EUR][1000 genomes]
rs7487150	0.96[ASN][1000 genomes]
rs7487645	0.86[EUR][1000 genomes]
rs7953880	0.86[EUR][1000 genomes]
rs7955310	0.90[EUR][1000 genomes]
rs7959129	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7964642	0.96[ASN][1000 genomes]
rs7969251	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7978443	0.86[EUR][1000 genomes]
rs7979184	0.81[EUR][1000 genomes]
rs7979474	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs829125	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs829133	0.83[JPT][hapmap]
rs865490	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs939631	1.00[CEU][hapmap];0.89[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs951591	1.00[CEU][hapmap];0.89[CHB][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes]
rs9634264	0.90[EUR][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	esv3497481	chr12:51150734-51185125	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	30 gene(s)	inside rSNPs	diseases
2	esv3497482	chr12:51151798-51185232	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	30 gene(s)	inside rSNPs	diseases
3	esv3386327	chr12:51154734-51184232	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	30 gene(s)	inside rSNPs	diseases
4	nsv899077	chr12:51160612-51188397	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51159000-51175200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:51159000-51180200	Weak transcription	Esophagus	oesophagus
3	chr12:51159200-51174600	Weak transcription	Lung	lung
4	chr12:51159200-51179400	Weak transcription	Aorta	Aorta
5	chr12:51159200-51192600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:51159400-51192600	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr12:51159600-51189200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr12:51159800-51173800	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr12:51159800-51176200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr12:51159800-51178200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr12:51159800-51178400	Weak transcription	NHDF-Ad	bronchial
12	chr12:51159800-51180600	Weak transcription	Fetal Lung	lung
13	chr12:51159800-51189600	Weak transcription	Spleen	Spleen
14	chr12:51159800-51190400	Weak transcription	Fetal Kidney	kidney
15	chr12:51159800-51191200	Weak transcription	Rectal Smooth Muscle	rectum
16	chr12:51160000-51174800	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr12:51160000-51174800	Weak transcription	Osteobl	bone
18	chr12:51160000-51175000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr12:51160000-51179200	Weak transcription	HSMMtube	muscle
20	chr12:51160000-51179800	Weak transcription	Small Intestine	intestine
21	chr12:51160000-51189800	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr12:51160000-51190800	Weak transcription	Right Ventricle	heart
23	chr12:51160200-51172800	Weak transcription	HSMM	muscle
24	chr12:51160200-51174200	Weak transcription	Left Ventricle	heart
25	chr12:51160200-51175000	Weak transcription	Brain Anterior Caudate	brain
26	chr12:51160200-51178200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr12:51160200-51178400	Weak transcription	HMEC	breast
28	chr12:51160200-51179400	Weak transcription	Right Atrium	heart
29	chr12:51160200-51180200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr12:51160200-51189600	Weak transcription	Pancreas	Pancrea
31	chr12:51160200-51189800	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr12:51160600-51178200	Weak transcription	Psoas Muscle	Psoas
33	chr12:51160800-51174800	Weak transcription	Liver	Liver
34	chr12:51160800-51189600	Weak transcription	Brain Angular Gyrus	brain
35	chr12:51160800-51190600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr12:51161000-51175200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr12:51161000-51178200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr12:51161000-51189800	Weak transcription	Ovary	ovary
39	chr12:51161600-51175200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr12:51161800-51180400	Weak transcription	Colonic Mucosa	Colon
41	chr12:51162400-51179200	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr12:51162600-51175200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr12:51162600-51178800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr12:51163000-51178000	Weak transcription	A549	lung
45	chr12:51163000-51178400	Weak transcription	NHEK	skin
46	chr12:51163200-51175600	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr12:51163200-51179800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr12:51163400-51175000	Weak transcription	K562	blood
49	chr12:51164000-51174800	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr12:51164400-51189600	Weak transcription	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links