Variant report

Variant	rs12474331
Chromosome Location	chr2:37877664-37877665
allele	A/G
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	POLR2A	chr2:37877394-37878280	GM12892	blood:	n/a	n/a
2	POLR2A	chr2:37867842-37879116	U87	brain:	n/a	n/a
3	POLR2A	chr2:37877475-37879091	GM12878	blood:	n/a	n/a
4	POLR2A	chr2:37876706-37879046	GM12891	blood:	n/a	n/a
5	POLR2A	chr2:37876699-37878972	GM12878	blood:	n/a	n/a
6	WRNIP1	chr2:37877609-37878004	GM12878	blood:	n/a	n/a
7	POLR2A	chr2:37877212-37879204	GM12892	blood:	n/a	n/a
8	NFATC1	chr2:37877623-37878389	GM12878	blood:	n/a	n/a
9	POLR2A	chr2:37877155-37878139	GM12891	blood:	n/a	n/a
10	POLR2A	chr2:37876498-37878311	GM12878	blood:	n/a	n/a
11	POLR2A	chr2:37877148-37878228	GM12891	blood:	n/a	n/a
12	POLR2A	chr2:37874425-37878298	GM12891	blood:	n/a	n/a
13	POLR2A	chr2:37872360-37878906	U87	brain:	n/a	n/a
14	POLR2A	chr2:37876738-37879052	GM12878	blood:	n/a	n/a
15	POLR2A	chr2:37877650-37878688	U87	brain:	n/a	n/a
16	POLR2A	chr2:37877562-37879012	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:37877216..37879655-chr2:37884753..37886765,2	MCF-7	breast:
2	chr2:37877539..37880523-chr2:37887000..37889009,2	K562	blood:

Variant related genes	Relation type
CDC42EP3	TF binding region

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12469780	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17523989	0.83[AMR][1000 genomes]
rs3926381	0.88[ASN][1000 genomes]
rs4670746	0.90[CHB][hapmap];0.83[JPT][hapmap];0.88[ASN][1000 genomes]
rs4670750	0.87[JPT][hapmap]
rs4670756	1.00[AFR][1000 genomes]
rs4670758	0.84[AMR][1000 genomes]
rs4670760	0.82[AMR][1000 genomes]
rs56344180	0.86[ASN][1000 genomes]
rs57048603	0.90[AMR][1000 genomes]
rs6711909	0.83[JPT][hapmap]
rs6752119	0.83[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757793	chr2:37796654-38138939	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	esv2759043	chr2:37796654-38138939	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv833825	chr2:37808169-37985917	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv535645	chr2:37853282-37972640	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv535646	chr2:37853282-38014428	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
6	nsv873880	chr2:37868214-37926046	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
7	nsv535647	chr2:37874563-38014428	Enhancers Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:37853600-37897400	Weak transcription	Small Intestine	intestine
2	chr2:37860800-37879600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr2:37864200-37880200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr2:37864400-37879400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr2:37866800-37881000	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr2:37867000-37880600	Genic enhancers	Muscle Satellite Cultured Cells	--
7	chr2:37868600-37879800	Genic enhancers	Primary monocytes fromperipheralblood	blood
8	chr2:37870800-37878600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr2:37871400-37880600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr2:37872000-37892400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr2:37872200-37881800	Weak transcription	Fetal Kidney	kidney
12	chr2:37872400-37880800	Weak transcription	Fetal Brain Male	brain
13	chr2:37873000-37881400	Enhancers	Right Atrium	heart
14	chr2:37873600-37879600	Weak transcription	Gastric	stomach
15	chr2:37873600-37879600	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr2:37873600-37880200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr2:37873600-37881000	Weak transcription	Ovary	ovary
18	chr2:37873800-37889000	Enhancers	Primary T helper cells fromperipheralblood	blood
19	chr2:37874200-37881600	Genic enhancers	NHLF	lung
20	chr2:37874400-37881600	Enhancers	Psoas Muscle	Psoas
21	chr2:37874400-37883200	Enhancers	Adipose Nuclei	Adipose
22	chr2:37874600-37884000	Enhancers	Fetal Muscle Leg	muscle
23	chr2:37874600-37893000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr2:37874800-37880000	Genic enhancers	Lung	lung
25	chr2:37874800-37882000	Enhancers	Left Ventricle	heart
26	chr2:37875000-37878600	Genic enhancers	HMEC	breast
27	chr2:37875200-37877800	Enhancers	Fetal Heart	heart
28	chr2:37875200-37878000	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr2:37875200-37879400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr2:37875200-37881800	Enhancers	Spleen	Spleen
31	chr2:37875200-37882200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr2:37875400-37879400	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr2:37875400-37881200	Enhancers	Primary B cells from peripheral blood	blood
34	chr2:37875400-37883400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr2:37875600-37878200	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr2:37875600-37879200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
37	chr2:37875600-37881000	Weak transcription	Fetal Brain Female	brain
38	chr2:37875600-37881200	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr2:37875800-37879400	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr2:37875800-37879400	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr2:37875800-37879600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr2:37875800-37879600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr2:37875800-37880400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr2:37875800-37881000	Weak transcription	Brain Germinal Matrix	brain
45	chr2:37875800-37881600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr2:37875800-37882000	Enhancers	Right Ventricle	heart
47	chr2:37875800-37883800	Genic enhancers	NHDF-Ad	bronchial
48	chr2:37875800-37884400	Weak transcription	Brain Cingulate Gyrus	brain
49	chr2:37875800-37891800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
50	chr2:37875800-37893600	Weak transcription	Fetal Intestine Large	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links