Variant report

Variant	rs3764902
Chromosome Location	chr7:66098582-66098583
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs12531402	1.00[JPT][hapmap]
rs12532147	1.00[JPT][hapmap]
rs12532267	1.00[JPT][hapmap]
rs12534391	1.00[JPT][hapmap]
rs12534985	1.00[JPT][hapmap]
rs12536818	0.82[JPT][hapmap]
rs12537403	1.00[JPT][hapmap]
rs12539848	1.00[JPT][hapmap]
rs2286682	1.00[JPT][hapmap]
rs3735146	1.00[JPT][hapmap]
rs3778906	1.00[JPT][hapmap]
rs3778911	1.00[JPT][hapmap]
rs3800813	1.00[JPT][hapmap]
rs3823608	0.85[JPT][hapmap]
rs4717305	1.00[JPT][hapmap]
rs4717311	1.00[JPT][hapmap]
rs4718382	1.00[JPT][hapmap]
rs4718390	1.00[JPT][hapmap]
rs4718391	1.00[JPT][hapmap]
rs4718398	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532124	chr7:65371521-66234730	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	125 gene(s)	inside rSNPs	diseases
2	nsv1026559	chr7:65617368-66370805	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
3	nsv1035107	chr7:65814901-66114919	Genic enhancers Strong transcription ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
4	nsv538909	chr7:65814901-66114919	Strong transcription Weak transcription Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
5	esv2761151	chr7:66095738-66138285	Flanking Active TSS Strong transcription Genic enhancers Active TSS Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3764902	RABGEF1	cis	multi-tissue	Pritchard
rs3764902	RABGEF1	Cis_1M	lymphoblastoid	RTeQTL
rs3764902	hmm32897	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66094400-66103200	Weak transcription	Small Intestine	intestine
2	chr7:66094800-66103400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr7:66095000-66099200	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr7:66095000-66099400	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr7:66095000-66099400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
6	chr7:66095000-66099400	Weak transcription	Aorta	Aorta
7	chr7:66095000-66099600	Weak transcription	A549	lung
8	chr7:66095000-66101000	Weak transcription	NHEK	skin
9	chr7:66095000-66102400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr7:66095000-66103000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr7:66095000-66103000	Weak transcription	Fetal Kidney	kidney
12	chr7:66095000-66103000	Weak transcription	Fetal Lung	lung
13	chr7:66095000-66103200	Weak transcription	Psoas Muscle	Psoas
14	chr7:66095000-66103400	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr7:66095000-66103400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr7:66095000-66103400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr7:66095000-66104200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr7:66095000-66108800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr7:66095000-66109000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr7:66095000-66115200	Weak transcription	HMEC	breast
21	chr7:66095200-66098600	Weak transcription	Liver	Liver
22	chr7:66095200-66099000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr7:66095200-66099400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr7:66095200-66099400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr7:66095200-66099800	Weak transcription	Colonic Mucosa	Colon
26	chr7:66095200-66101000	Weak transcription	NHDF-Ad	bronchial
27	chr7:66095200-66103000	Weak transcription	Stomach Mucosa	stomach
28	chr7:66095200-66103200	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr7:66095200-66118400	Weak transcription	Fetal Heart	heart
30	chr7:66095200-66118400	Weak transcription	HUVEC	blood vessel
31	chr7:66095400-66099400	Weak transcription	Colon Smooth Muscle	Colon
32	chr7:66095400-66101000	Weak transcription	NH-A	brain
33	chr7:66095400-66103200	Weak transcription	Pancreas	Pancrea
34	chr7:66095800-66099200	Weak transcription	Brain Substantia Nigra	brain
35	chr7:66095800-66100800	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr7:66095800-66101000	Weak transcription	HSMM	muscle
37	chr7:66095800-66101000	Weak transcription	K562	blood
38	chr7:66095800-66102800	Weak transcription	Fetal Brain Male	brain
39	chr7:66095800-66103200	Weak transcription	Esophagus	oesophagus
40	chr7:66096000-66099400	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr7:66096000-66113800	Strong transcription	Fetal Stomach	stomach
42	chr7:66096200-66099200	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr7:66096200-66101000	Weak transcription	NHLF	lung
44	chr7:66097000-66098800	Enhancers	Primary T helper naive cells from peripheral blood	blood
45	chr7:66097000-66099000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
46	chr7:66097000-66099400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr7:66097000-66113400	Strong transcription	Fetal Brain Female	brain
48	chr7:66097200-66098800	Weak transcription	Fetal Thymus	thymus
49	chr7:66097200-66099200	Weak transcription	Brain Anterior Caudate	brain
50	chr7:66097200-66099200	Weak transcription	Duodenum Smooth Muscle	Duodenum

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