Variant report

Variant	rs2873950
Chromosome Location	chr3:119547062-119547063
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:119546502..119549235-chr3:119813550..119815465,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000242622	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10433404	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10934500	0.93[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10934502	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10934503	0.93[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1154595	0.82[JPT][hapmap]
rs11915717	0.93[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.91[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11917714	0.80[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12054090	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12108149	0.88[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12629015	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12634476	1.00[CEU][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12634889	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12638973	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13321783	0.82[JPT][hapmap]
rs1574154	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16830567	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1719894	0.82[JPT][hapmap]
rs1732170	0.86[JPT][hapmap]
rs1980718	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2276707	1.00[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2319398	0.82[JPT][hapmap]
rs2319399	0.82[JPT][hapmap]
rs28536662	0.82[JPT][hapmap]
rs28831519	0.89[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs3107669	0.82[JPT][hapmap]
rs3732359	0.82[JPT][hapmap];0.86[TSI][hapmap]
rs3732360	0.82[JPT][hapmap]
rs3732361	0.86[JPT][hapmap]
rs3814057	1.00[CEU][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3814058	1.00[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4261913	0.87[JPT][hapmap]
rs4340737	0.93[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4624596	0.93[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4688042	0.93[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4688046	0.93[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4688047	0.93[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4688054	0.93[ASW][hapmap];1.00[CEU][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap]
rs56728675	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57939147	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58493895	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60389731	0.95[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs60393216	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62264706	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62264708	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62264714	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62264734	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62264739	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62264742	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62264743	0.91[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6438552	0.82[JPT][hapmap]
rs6438553	0.82[JPT][hapmap]
rs6773751	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6782799	0.85[JPT][hapmap]
rs6784598	0.86[JPT][hapmap]
rs6792572	0.82[JPT][hapmap]
rs6795653	0.82[JPT][hapmap]
rs6797459	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6800622	0.82[JPT][hapmap]
rs6805251	0.86[JPT][hapmap]
rs6808874	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7431209	0.81[JPT][hapmap]
rs7633279	0.91[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7639388	1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7644234	0.82[JPT][hapmap]
rs9813864	0.86[JPT][hapmap]
rs9873477	0.82[JPT][hapmap]
rs9878473	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011178	chr3:119437192-119589116	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv536703	chr3:119437192-119589116	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119529400-119566600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr3:119529600-119582000	Weak transcription	Spleen	Spleen
3	chr3:119532400-119551000	Weak transcription	Right Ventricle	heart
4	chr3:119534800-119558600	Weak transcription	Colonic Mucosa	Colon
5	chr3:119536200-119569000	Weak transcription	Esophagus	oesophagus
6	chr3:119536400-119570200	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr3:119536600-119576000	Weak transcription	Fetal Muscle Trunk	muscle
8	chr3:119536600-119576400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr3:119537000-119548200	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr3:119537200-119550600	Weak transcription	Fetal Heart	heart
11	chr3:119538600-119550800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr3:119539000-119550800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr3:119539000-119576400	Weak transcription	Ovary	ovary
14	chr3:119540400-119547600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr3:119540400-119563600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr3:119540400-119574800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr3:119540400-119576600	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr3:119540600-119548000	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr3:119540800-119547200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr3:119540800-119577000	Weak transcription	Aorta	Aorta
21	chr3:119541000-119548200	Weak transcription	Brain Cingulate Gyrus	brain
22	chr3:119541000-119581600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr3:119541200-119561800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr3:119541200-119587000	Weak transcription	Gastric	stomach
25	chr3:119541800-119559200	Weak transcription	Pancreas	Pancrea
26	chr3:119541800-119560000	Weak transcription	Rectal Smooth Muscle	rectum
27	chr3:119542200-119548400	Weak transcription	Colon Smooth Muscle	Colon
28	chr3:119542200-119550600	Weak transcription	NH-A	brain
29	chr3:119542400-119581200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr3:119542600-119548000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr3:119542600-119560800	Weak transcription	Hela-S3	cervix
32	chr3:119542600-119581600	Weak transcription	HUVEC	blood vessel
33	chr3:119542800-119575000	Weak transcription	Fetal Kidney	kidney
34	chr3:119543200-119548800	Weak transcription	Fetal Brain Male	brain
35	chr3:119543400-119548600	Strong transcription	Primary T cells from cord blood	blood
36	chr3:119543400-119549000	Weak transcription	Brain Substantia Nigra	brain
37	chr3:119543800-119548000	Weak transcription	Stomach Mucosa	stomach
38	chr3:119544000-119561800	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr3:119544600-119547600	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr3:119545000-119550800	Weak transcription	A549	lung
41	chr3:119545000-119551800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr3:119545000-119559600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr3:119545000-119576400	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr3:119545200-119548200	Weak transcription	Brain Hippocampus Middle	brain
45	chr3:119545200-119550600	Weak transcription	HSMMtube	muscle
46	chr3:119545200-119552000	Weak transcription	Primary hematopoietic stem cells	blood
47	chr3:119545200-119559200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr3:119545200-119559400	Weak transcription	Primary T helper cells PMA-I stimulated	--
49	chr3:119545200-119561600	Weak transcription	Fetal Stomach	stomach
50	chr3:119545200-119562800	Weak transcription	NHLF	lung

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