Variant report

Variant	rs3796092
Chromosome Location	chr2:234390469-234390470
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:234390304-234390943	PANC-1	pancreas:	n/a	n/a
2	POLR2A	chr2:234390359-234390617	K562	blood:	n/a	n/a
3	POLR2A	chr2:234390313-234390676	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr2:234388311-234391938	A549	lung:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:234388753..234400184-chr2:234596527..234603213,35	MCF-7	breast:
2	chr2:234386983..234399433-chr2:234613282..234621553,23	MCF-7	breast:
3	chr2:234387565..234390486-chr2:234761608..234763193,2	MCF-7	breast:
4	chr2:234387197..234390730-chr2:234600088..234603557,3	MCF-7	breast:
5	chr2:234356161..234358499-chr2:234388405..234391243,2	MCF-7	breast:
6	chr2:234388450..234390817-chr2:234616855..234619470,2	MCF-7	breast:
7	chr2:234389092..234391362-chr2:234473035..234476486,3	MCF-7	breast:

No data

Variant related genes	Relation type
USP40	TF binding region
ENSG00000167165	Chromatin interaction
ENSG00000123485	Chromatin interaction
ENSG00000077044	Chromatin interaction
ENSG00000224814	Chromatin interaction
ENSG00000085982	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1046976	1.00[CHB][hapmap]
rs10929178	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11675254	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs11675858	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11676524	0.83[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.86[LWK][hapmap];0.90[MEX][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11686188	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11694406	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs2228939	0.86[AMR][1000 genomes]
rs3754595	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs3768801	0.83[AMR][1000 genomes]
rs3768802	0.83[AMR][1000 genomes]
rs3796090	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes]
rs3820744	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs3828307	1.00[CHB][hapmap]
rs4047189	0.83[ASW][hapmap];0.85[CEU][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];0.86[LWK][hapmap];0.90[MEX][hapmap];0.98[MKK][hapmap];0.94[TSI][hapmap];0.85[YRI][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6704644	0.92[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6746234	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.90[MEX][hapmap];0.91[MKK][hapmap];0.94[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6753242	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs72980376	0.86[AMR][1000 genomes]
rs72980395	0.95[EUR][1000 genomes]
rs72980402	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72982309	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72982316	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72982325	0.88[EUR][1000 genomes]
rs7587876	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs7598771	0.85[CEU][hapmap];1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529419	chr2:234229606-234670426	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	nsv1000870	chr2:234333083-234410768	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv876013	chr2:234338227-234579915	Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	nsv3214	chr2:234384436-234416949	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3796092	ECEL1P2	cis	parietal	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234339600-234394200	Weak transcription	HUVEC	blood vessel
2	chr2:234339800-234391400	Weak transcription	NHDF-Ad	bronchial
3	chr2:234343000-234393000	Strong transcription	Primary T cells from cord blood	blood
4	chr2:234343000-234402200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr2:234363800-234390600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr2:234364000-234411200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:234365800-234393600	Weak transcription	Hela-S3	cervix
8	chr2:234373000-234392200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr2:234373000-234409800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr2:234373400-234391000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr2:234373800-234404400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr2:234375400-234411200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr2:234377800-234391400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr2:234377800-234397200	Weak transcription	Small Intestine	intestine
15	chr2:234378200-234395000	Weak transcription	Right Atrium	heart
16	chr2:234378400-234390800	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr2:234378400-234391000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr2:234378600-234391600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr2:234378800-234391400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr2:234379000-234391200	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr2:234380800-234395000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr2:234381200-234394800	Strong transcription	Pancreas	Pancrea
23	chr2:234381600-234391000	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr2:234381600-234393400	Weak transcription	Primary hematopoietic stem cells	blood
25	chr2:234381600-234399600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr2:234382000-234391600	Weak transcription	GM12878-XiMat	blood
27	chr2:234383000-234395000	Strong transcription	NHLF	lung
28	chr2:234383400-234391200	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr2:234383400-234391400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr2:234383400-234395400	Strong transcription	Brain Hippocampus Middle	brain
31	chr2:234383400-234400200	Strong transcription	Fetal Intestine Small	intestine
32	chr2:234384000-234392800	Strong transcription	Thymus	Thymus
33	chr2:234384000-234395200	Strong transcription	Liver	Liver
34	chr2:234384000-234412400	Weak transcription	Fetal Heart	heart
35	chr2:234384200-234391600	Strong transcription	Sigmoid Colon	Sigmoid Colon
36	chr2:234384200-234392800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr2:234384200-234394400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr2:234384200-234394400	Strong transcription	Placenta	Placenta
39	chr2:234384200-234394600	Strong transcription	Fetal Thymus	thymus
40	chr2:234384200-234394800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr2:234384200-234394800	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr2:234384200-234395000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr2:234384400-234391800	Strong transcription	Ovary	ovary
44	chr2:234384400-234395000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr2:234384400-234395000	Strong transcription	Left Ventricle	heart
46	chr2:234384400-234398200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr2:234384400-234402200	Strong transcription	Rectal Mucosa Donor 29	rectum
48	chr2:234384400-234402600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr2:234384600-234392800	Strong transcription	Right Ventricle	heart
50	chr2:234384600-234395000	Strong transcription	Brain Cingulate Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links