Variant report

Variant	rs3858637
Chromosome Location	chr12:51694595-51694596
allele	A/C
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	EGR1	chr12:51694508-51694868	HCT-116	colon:	n/a	n/a
2	POLR2A	chr12:51694426-51695731	K562	blood:	n/a	n/a
3	EGR1	chr12:51694561-51694836	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:51636888..51638953-chr12:51693663..51695699,2	K562	blood:
2	chr12:51691403..51693767-chr12:51694512..51696537,2	K562	blood:

Variant related genes	Relation type
BIN2	TF binding region

Extended variants
information (count: 55 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10876156	0.80[CEU][hapmap]
rs11341	1.00[CEU][hapmap]
rs12578771	0.90[EUR][1000 genomes]
rs12580302	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12581282	0.90[EUR][1000 genomes]
rs17860287	0.83[EUR][1000 genomes]
rs17860296	0.85[EUR][1000 genomes]
rs17860299	0.93[CEU][hapmap];0.85[TSI][hapmap]
rs17860302	0.85[EUR][1000 genomes]
rs17860317	0.93[CEU][hapmap]
rs17860346	0.81[EUR][1000 genomes]
rs17860365	0.81[EUR][1000 genomes]
rs17860380	0.81[EUR][1000 genomes]
rs17860382	0.81[EUR][1000 genomes]
rs17860387	0.81[EUR][1000 genomes]
rs1991433	0.85[EUR][1000 genomes]
rs2114876	0.82[EUR][1000 genomes]
rs2288367	0.93[CEU][hapmap];0.89[CHB][hapmap];0.84[CHD][hapmap];0.83[GIH][hapmap];0.88[JPT][hapmap];0.92[TSI][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3782470	0.93[CEU][hapmap]
rs3969069	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs4477479	0.82[EUR][1000 genomes]
rs4611251	0.82[EUR][1000 genomes]
rs4761881	0.93[CEU][hapmap]
rs4761982	0.82[EUR][1000 genomes]
rs4761985	0.82[EUR][1000 genomes]
rs55901988	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs57484374	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs58213562	0.90[EUR][1000 genomes]
rs58673573	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs60641385	0.90[EUR][1000 genomes]
rs60797544	0.91[EUR][1000 genomes]
rs61172662	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61380773	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61570206	0.90[EUR][1000 genomes]
rs61605107	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6580821	0.86[CEU][hapmap];0.88[JPT][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes]
rs7133314	0.85[CEU][hapmap];0.88[JPT][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes]
rs7135736	0.86[CEU][hapmap];0.88[JPT][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes]
rs7138394	0.91[EUR][1000 genomes]
rs7308177	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7311196	1.00[CEU][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.85[TSI][hapmap]
rs7312857	1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7316221	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7316301	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7316604	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs74093810	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs74093814	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs74093823	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs74093827	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs74093853	0.86[EUR][1000 genomes]
rs7954976	0.86[CEU][hapmap];0.88[JPT][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes]
rs7975715	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]

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	nsv482304	chr12:51653496-51814917	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv469377	chr12:51690751-51733951	Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv558877	chr12:51690751-51733951	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3858637	FAM186B	cis	parietal	SCAN
rs3858637	COL2A1	cis	parietal	SCAN
rs3858637	LOC57228	cis	multi-tissue	Pritchard
rs3858637	ZNF641	cis	cerebellum	SCAN
rs3858637	ELA1	cis	multi-tissue	Pritchard

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51673800-51697600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr12:51674000-51698400	Strong transcription	Fetal Thymus	thymus
3	chr12:51674000-51701400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr12:51674200-51704000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr12:51674400-51698400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr12:51674400-51698600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr12:51674400-51698800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr12:51674400-51700600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr12:51678000-51697600	Weak transcription	Adipose Nuclei	Adipose
10	chr12:51680600-51701600	Weak transcription	Small Intestine	intestine
11	chr12:51681200-51696600	Strong transcription	Primary T cells fromperipheralblood	blood
12	chr12:51681800-51714200	Weak transcription	Gastric	stomach
13	chr12:51685800-51697600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr12:51686200-51702800	Weak transcription	Colonic Mucosa	Colon
15	chr12:51686600-51698800	Strong transcription	Primary B cells from peripheral blood	blood
16	chr12:51686800-51698600	Strong transcription	Primary T cells from cord blood	blood
17	chr12:51686800-51701200	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr12:51687000-51703800	Strong transcription	Primary neutrophils fromperipheralblood	blood
19	chr12:51687000-51707400	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr12:51687200-51696800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr12:51687200-51697200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
22	chr12:51687800-51697200	Strong transcription	Primary T helper cells fromperipheralblood	blood
23	chr12:51687800-51700000	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr12:51687800-51708000	Strong transcription	Thymus	Thymus
25	chr12:51688000-51698400	Strong transcription	Primary T helper cells PMA-I stimulated	--
26	chr12:51688800-51696800	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr12:51689600-51696000	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr12:51691000-51696800	Strong transcription	Placenta	Placenta
29	chr12:51691800-51702200	Weak transcription	Rectal Smooth Muscle	rectum
30	chr12:51692600-51698200	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr12:51692800-51698400	Strong transcription	Primary T killer memory cells from peripheral blood	blood
32	chr12:51692800-51698600	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr12:51693000-51695000	Strong transcription	Spleen	Spleen
34	chr12:51693000-51697200	Strong transcription	Primary hematopoietic stem cells	blood
35	chr12:51693000-51698000	Strong transcription	GM12878-XiMat	blood
36	chr12:51693000-51698400	Strong transcription	Primary B cells from cord blood	blood
37	chr12:51693400-51696400	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr12:51693800-51701600	Weak transcription	Duodenum Mucosa	Duodenum
39	chr12:51694200-51694800	Strong transcription	Rectal Mucosa Donor 29	rectum
40	chr12:51694200-51694800	Enhancers	K562	blood

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