Variant report

Variant	rs13316457
Chromosome Location	chr3:23992415-23992416
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:23954505..23971330-chr3:23977357..23992645,61	MCF-7	breast:
2	chr3:23992186..23994310-chr3:24012801..24015062,2	MCF-7	breast:
3	chr3:23956631..23966740-chr3:23975650..23993173,64	MCF-7	breast:
4	chr3:23985538..23993367-chr3:23993730..24003801,19	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197885	Chromatin interaction
ENSG00000174748	Chromatin interaction
ENSG00000174738	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10084748	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1037635	1.00[ASN][1000 genomes]
rs11129128	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13070128	1.00[ASN][1000 genomes]
rs13087250	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13317815	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13321439	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13321440	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1533141	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1567579	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1567580	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28524116	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34036067	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34058540	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34082882	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34593533	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34866549	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34953164	1.00[ASN][1000 genomes]
rs35136361	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35457462	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35755171	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35755253	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36063721	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36089963	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3762775	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3935253	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4131404	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4300960	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4490300	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4535169	1.00[ASN][1000 genomes]
rs4602333	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858096	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858554	1.00[ASN][1000 genomes]
rs4858556	1.00[ASN][1000 genomes]
rs4858564	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55932805	1.00[ASN][1000 genomes]
rs6550808	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66609380	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67002637	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67236598	1.00[ASN][1000 genomes]
rs67606949	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6767005	1.00[ASN][1000 genomes]
rs6770052	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6775878	1.00[ASN][1000 genomes]
rs6776201	1.00[ASN][1000 genomes]
rs6776568	1.00[ASN][1000 genomes]
rs6778577	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6790140	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6791805	1.00[ASN][1000 genomes]
rs6803214	1.00[ASN][1000 genomes]
rs6803587	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs71324126	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73150266	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73150299	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7610689	1.00[ASN][1000 genomes]
rs7610935	1.00[ASN][1000 genomes]
rs7611018	1.00[ASN][1000 genomes]
rs954748	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9809225	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9812419	1.00[ASN][1000 genomes]
rs9812870	0.82[EUR][1000 genomes]
rs9817923	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9853954	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9855481	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9859567	1.00[ASN][1000 genomes]
rs9863176	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9875577	1.00[ASN][1000 genomes]
rs9882067	1.00[ASN][1000 genomes]
rs9883834	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv533980	chr3:23445901-24311972	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv834638	chr3:23963860-24117191	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23988000-23995000	Weak transcription	Spleen	Spleen
2	chr3:23988200-23993800	Enhancers	Brain Substantia Nigra	brain
3	chr3:23988200-24000600	Weak transcription	Fetal Brain Male	brain
4	chr3:23988200-24003600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr3:23988400-23993600	Enhancers	Primary T killer memory cells from peripheral blood	blood
6	chr3:23988400-23995200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr3:23988400-23996000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
8	chr3:23988400-23996400	Enhancers	Primary T helper naive cells from peripheral blood	blood
9	chr3:23988400-24003000	Weak transcription	Fetal Muscle Trunk	muscle
10	chr3:23988400-24003400	Weak transcription	Fetal Kidney	kidney
11	chr3:23988600-23994000	Enhancers	Psoas Muscle	Psoas
12	chr3:23988600-23996000	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr3:23989000-23993800	Enhancers	Liver	Liver
14	chr3:23989000-23996400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr3:23989000-23997800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr3:23989000-23998200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr3:23989200-23992800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr3:23989200-23995000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr3:23989200-23996000	Enhancers	Adipose Nuclei	Adipose
20	chr3:23989200-23996200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr3:23989200-23996200	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr3:23989200-24000600	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr3:23989200-24003000	Weak transcription	Fetal Thymus	thymus
24	chr3:23989200-24007400	Weak transcription	Fetal Brain Female	brain
25	chr3:23989200-24018000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr3:23989200-24020600	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr3:23989200-24033200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr3:23989400-23992800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr3:23989400-23993800	Enhancers	Brain Anterior Caudate	brain
30	chr3:23989400-23994400	Enhancers	Brain Angular Gyrus	brain
31	chr3:23989400-23996000	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr3:23989400-23996200	Enhancers	Brain Hippocampus Middle	brain
33	chr3:23989600-24003400	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr3:23989600-24003400	Weak transcription	Esophagus	oesophagus
35	chr3:23989600-24003600	Weak transcription	Colonic Mucosa	Colon
36	chr3:23989800-23993200	Weak transcription	Brain Germinal Matrix	brain
37	chr3:23989800-23993400	Weak transcription	Gastric	stomach
38	chr3:23989800-23994600	Weak transcription	Lung	lung
39	chr3:23989800-23995600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
40	chr3:23989800-23996000	Weak transcription	Osteobl	bone
41	chr3:23989800-24017800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr3:23990000-24000200	Weak transcription	HUVEC	blood vessel
43	chr3:23990000-24001000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr3:23990400-23995400	Weak transcription	Aorta	Aorta
45	chr3:23990400-23996200	Weak transcription	Placenta	Placenta
46	chr3:23990400-23997600	Weak transcription	NH-A	brain
47	chr3:23990600-23992800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr3:23990600-23995600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
49	chr3:23990600-23999800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr3:23990800-23995800	Enhancers	Primary B cells from cord blood	blood

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