Variant report

Variant	rs3770949
Chromosome Location	chr2:36603763-36603764
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	chr2:36603055-36603811	HUVEC	blood vessel:	n/a	n/a
2	NFIC	chr2:36603286-36603798	HepG2	liver:	n/a	n/a
3	NFIC	chr2:36603159-36603870	HepG2	liver:	n/a	n/a
4	REST	chr2:36603491-36603774	SK-N-SH	brain:	n/a	n/a
5	FOXA1	chr2:36602693-36603780	HepG2	liver:	n/a	n/a
6	NFIC	chr2:36603176-36604765	SK-N-SH	brain:	n/a	n/a
7	BCL3	chr2:36603182-36604671	A549	lung:	n/a	chr2:36604289-36604297
8	POLR2A	chr2:36603673-36604272	IMR90	lung:	n/a	n/a
9	KAP1	chr2:36603355-36603844	U2OS	brain:	n/a	n/a
10	POLR2A	chr2:36602871-36604603	PANC-1	pancreas:	n/a	n/a
11	TCF12	chr2:36603062-36604732	A549	lung:	n/a	chr2:36604301-36604308
12	EP300	chr2:36603280-36603810	HepG2	liver:	n/a	n/a
13	FOXA1	chr2:36603244-36603866	HepG2	liver:	n/a	n/a
14	TBP	chr2:36603559-36603974	H1-hESC	embryonic stem cell:	n/a	n/a
15	MAX	chr2:36603237-36604715	A549	lung:	n/a	n/a
16	MYBL2	chr2:36603207-36603906	HepG2	liver:	n/a	n/a
17	GATA3	chr2:36603180-36604812	SK-N-SH	brain:	n/a	n/a
18	SP1	chr2:36603244-36604745	A549	lung:	n/a	chr2:36603618-36603632
19	PBX3	chr2:36603352-36604830	SK-N-SH	brain:	n/a	n/a
20	POLR2A	chr2:36602922-36605915	HUVEC	blood vessel:	n/a	n/a
21	FOXA2	chr2:36603368-36603810	HepG2	liver:	n/a	n/a
22	REST	chr2:36603296-36604708	A549	lung:	n/a	chr2:36604290-36604299 chr2:36604330-36604350 chr2:36604293-36604306
23	POLR2A	chr2:36603561-36603777	HUVEC	blood vessel:	n/a	n/a
24	POLR2A	chr2:36603557-36603852	ProgFib	skin:	n/a	n/a
25	NFIC	chr2:36603286-36604001	ECC-1	luminal epithelium:	n/a	n/a
26	EP300	chr2:36603286-36604848	SK-N-SH	brain:	n/a	chr2:36603893-36603907
27	FOXA1	chr2:36603323-36603831	HepG2	liver:	n/a	n/a
28	POLR2A	chr2:36602829-36605623	HepG2	liver:	n/a	n/a
29	NFIC	chr2:36603249-36603952	ECC-1	luminal epithelium:	n/a	n/a
30	RCOR1	chr2:36603182-36604677	IMR90	lung:	n/a	n/a
31	TCF12	chr2:36603292-36604857	SK-N-SH	brain:	n/a	chr2:36604301-36604308
32	HDAC2	chr2:36603341-36603803	HepG2	liver:	n/a	n/a
33	GATA3	chr2:36603110-36604846	A549	lung:	n/a	n/a
34	FOXA1	chr2:36603243-36603786	HepG2	liver:	n/a	n/a
35	POLR2A	chr2:36603259-36603949	SK-N-SH	brain:	n/a	n/a
36	KAP1	chr2:36603310-36603764	HEK293	kidney:	n/a	n/a
37	POLR2A	chr2:36602824-36605829	A549	lung:	n/a	n/a
38	POLR2A	chr2:36603263-36605324	SK-N-SH	brain:	n/a	n/a
39	E2F4	chr2:36603565-36603902	MCF10A-Er-Src	breast:	n/a	n/a
40	POLR2A	chr2:36602709-36605505	HUVEC	blood vessel:	n/a	n/a
41	NR2F2	chr2:36603322-36603786	MCF-7	breast:	n/a	n/a
42	FOSL2	chr2:36603143-36604919	A549	lung:	n/a	n/a
43	POLR2A	chr2:36603291-36603823	PANC-1	pancreas:	n/a	n/a
44	TEAD4	chr2:36603237-36603930	HepG2	liver:	n/a	n/a
45	NFIC	chr2:36603321-36603923	SK-N-SH	brain:	n/a	n/a
46	TCF12	chr2:36603239-36604863	SK-N-SH	brain:	n/a	chr2:36604301-36604308
47	POLR2A	chr2:36602908-36605846	HUVEC	blood vessel:	n/a	n/a
48	FOXA2	chr2:36603307-36603986	A549	lung:	n/a	n/a
49	EP300	chr2:36603235-36604725	A549	lung:	n/a	chr2:36603893-36603907
50	FOXA2	chr2:36603443-36603883	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:36586071..36588141-chr2:36602497..36605299,2	MCF-7	breast:
2	chr2:36596157..36599052-chr2:36601566..36604769,3	MCF-7	breast:
3	chr2:36598192..36600031-chr2:36601938..36604063,3	MCF-7	breast:

Variant related genes	Relation type
CRIM1	TF binding region
ENSG00000150938	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10184083	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10184188	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11885390	1.00[JPT][hapmap]
rs11891181	1.00[JPT][hapmap]
rs12712499	0.84[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap];0.95[ASN][1000 genomes]
rs12712501	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs34582671	0.81[ASN][1000 genomes]
rs3770911	0.84[JPT][hapmap]
rs3770919	1.00[JPT][hapmap]
rs3770928	1.00[JPT][hapmap]
rs3770935	1.00[JPT][hapmap]
rs3770938	0.84[JPT][hapmap]
rs3770939	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs3770941	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs3770943	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs3770962	0.89[ASN][1000 genomes]
rs3821162	1.00[JPT][hapmap]
rs3821166	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4670145	1.00[JPT][hapmap]
rs4670553	1.00[JPT][hapmap]
rs67044425	0.81[ASN][1000 genomes]
rs67501694	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72785151	0.81[ASN][1000 genomes]
rs72785157	0.89[ASN][1000 genomes]
rs72785173	0.92[ASN][1000 genomes]
rs7556859	0.80[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833803	chr2:36589065-36745779	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:36586200-36626600	Weak transcription	Primary B cells from cord blood	blood
2	chr2:36592400-36605800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr2:36594200-36605400	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr2:36595200-36606000	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr2:36595600-36604200	Weak transcription	Fetal Muscle Trunk	muscle
6	chr2:36595600-36604400	Enhancers	Colon Smooth Muscle	Colon
7	chr2:36598400-36603800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:36598600-36607000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr2:36599000-36604000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr2:36599400-36609600	Enhancers	HMEC	breast
11	chr2:36599800-36605400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr2:36600000-36607200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr2:36600000-36609000	Genic enhancers	HSMM	muscle
14	chr2:36600400-36612000	Genic enhancers	Osteobl	bone
15	chr2:36600600-36608800	Genic enhancers	Muscle Satellite Cultured Cells	--
16	chr2:36600800-36607200	Weak transcription	Pancreas	Pancrea
17	chr2:36601000-36604000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr2:36601000-36604000	Weak transcription	Gastric	stomach
19	chr2:36601000-36604000	Enhancers	HUVEC	blood vessel
20	chr2:36601000-36604600	Enhancers	Hela-S3	cervix
21	chr2:36601000-36605400	Weak transcription	Aorta	Aorta
22	chr2:36601200-36605600	Enhancers	NHDF-Ad	bronchial
23	chr2:36601400-36604800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr2:36601800-36604200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr2:36602000-36604000	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr2:36602200-36604600	Enhancers	Duodenum Smooth Muscle	Duodenum
27	chr2:36602200-36604800	Enhancers	Rectal Mucosa Donor 31	rectum
28	chr2:36602400-36604400	Enhancers	NH-A	brain
29	chr2:36602400-36605000	Enhancers	Rectal Mucosa Donor 29	rectum
30	chr2:36602600-36604400	Enhancers	Cortex derived primary cultured neurospheres	brain
31	chr2:36602600-36605400	Enhancers	Skeletal Muscle Male	skeletal muscle
32	chr2:36602800-36604200	Enhancers	Liver	Liver
33	chr2:36602800-36604200	Enhancers	Fetal Lung	lung
34	chr2:36602800-36604400	Enhancers	Duodenum Mucosa	Duodenum
35	chr2:36602800-36604400	Enhancers	Sigmoid Colon	Sigmoid Colon
36	chr2:36602800-36604600	Enhancers	Fetal Kidney	kidney
37	chr2:36602800-36604800	Enhancers	Fetal Intestine Large	intestine
38	chr2:36602800-36604800	Enhancers	Rectal Smooth Muscle	rectum
39	chr2:36602800-36605000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
40	chr2:36603000-36603800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr2:36603000-36603800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr2:36603000-36604000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr2:36603000-36604000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr2:36603000-36604400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr2:36603000-36604400	Enhancers	Fetal Intestine Small	intestine
46	chr2:36603000-36604600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr2:36603000-36605200	Enhancers	Stomach Mucosa	stomach
48	chr2:36603200-36604200	Flanking Active TSS	HepG2	liver
49	chr2:36603200-36604400	Enhancers	Brain Cingulate Gyrus	brain
50	chr2:36603200-36604400	Enhancers	Placenta	Placenta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links