Variant report

Variant	rs3797207
Chromosome Location	chr5:95169909-95169910
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:94981172..94985318-chr5:95169805..95176246,5	MCF-7	breast:
2	chr5:95167615..95170613-chr5:95172553..95174092,2	MCF-7	breast:
3	chr5:95168597..95170209-chr5:95172089..95173618,2	K562	blood:
4	chr5:95156501..95159437-chr5:95167856..95170336,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000173221	Chromatin interaction
ENSG00000175449	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10055875	0.86[EUR][1000 genomes]
rs10067941	0.85[EUR][1000 genomes]
rs10079710	0.85[EUR][1000 genomes]
rs2161312	0.88[CEU][hapmap];0.88[CHD][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes]
rs3756705	1.00[CHB][hapmap]
rs41470049	0.88[CEU][hapmap];0.88[CHD][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes]
rs6420125	0.88[CEU][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes]
rs6556888	0.86[EUR][1000 genomes]
rs6882301	0.93[EUR][1000 genomes]
rs6883552	0.82[CHB][hapmap];0.88[CHD][hapmap]
rs6884979	0.83[CHD][hapmap]
rs7702848	0.88[CEU][hapmap];0.94[CHD][hapmap];0.94[TSI][hapmap];0.86[EUR][1000 genomes]
rs7716279	0.85[EUR][1000 genomes]
rs918470	0.83[CEU][hapmap]

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	nsv830409	chr5:95006686-95204496	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv1015180	chr5:95134357-95286446	Strong transcription Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv882389	chr5:95144952-95173887	Strong transcription Active TSS Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3797207	GLRX	cis	parietal	SCAN

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:95160600-95170000	Weak transcription	Right Atrium	heart
2	chr5:95160600-95170400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr5:95161600-95171400	Weak transcription	Small Intestine	intestine
4	chr5:95161800-95170000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr5:95164200-95171400	Weak transcription	Spleen	Spleen
6	chr5:95164800-95170200	Weak transcription	Colonic Mucosa	Colon
7	chr5:95164800-95170400	Weak transcription	Lung	lung
8	chr5:95167800-95170000	Enhancers	Primary T helper cells fromperipheralblood	blood
9	chr5:95167800-95170400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr5:95168000-95170400	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr5:95168200-95170000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr5:95168400-95170000	Enhancers	Liver	Liver
13	chr5:95168600-95170000	Enhancers	Primary T cells fromperipheralblood	blood
14	chr5:95168600-95170000	Enhancers	Stomach Mucosa	stomach
15	chr5:95168600-95170200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
16	chr5:95168800-95170000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr5:95168800-95170000	Enhancers	HepG2	liver
18	chr5:95168800-95170200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr5:95168800-95170400	Enhancers	Placenta	Placenta
20	chr5:95169000-95170000	Enhancers	Fetal Intestine Large	intestine
21	chr5:95169000-95170400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
22	chr5:95169200-95170200	Weak transcription	Fetal Thymus	thymus
23	chr5:95169200-95170400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr5:95169200-95170400	Weak transcription	Gastric	stomach
25	chr5:95169200-95170400	Weak transcription	Pancreas	Pancrea
26	chr5:95169400-95170200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
27	chr5:95169600-95170000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
28	chr5:95169600-95170000	Enhancers	Muscle Satellite Cultured Cells	--
29	chr5:95169600-95170000	Enhancers	Duodenum Smooth Muscle	Duodenum
30	chr5:95169600-95170000	Flanking Active TSS	A549	lung
31	chr5:95169600-95170200	Flanking Active TSS	Primary T cells from cord blood	blood
32	chr5:95169600-95170200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
33	chr5:95169600-95170200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr5:95169600-95170400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr5:95169600-95170400	Enhancers	Fetal Intestine Small	intestine
36	chr5:95169600-95170400	Flanking Active TSS	Dnd41	blood
37	chr5:95169800-95170000	Enhancers	ES-I3 Cell Line	embryonic stem cell
38	chr5:95169800-95170000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr5:95169800-95170000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
40	chr5:95169800-95170000	Flanking Active TSS	Primary hematopoietic stem cells	blood
41	chr5:95169800-95170000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
42	chr5:95169800-95170000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr5:95169800-95170000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr5:95169800-95170000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr5:95169800-95170000	Enhancers	Brain Anterior Caudate	brain
46	chr5:95169800-95170000	Enhancers	Brain Hippocampus Middle	brain
47	chr5:95169800-95170000	Flanking Active TSS	Duodenum Mucosa	Duodenum
48	chr5:95169800-95170000	Flanking Active TSS	Fetal Kidney	kidney
49	chr5:95169800-95170000	Flanking Active TSS	Psoas Muscle	Psoas
50	chr5:95169800-95170000	Enhancers	Rectal Mucosa Donor 31	rectum

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