Variant report

Variant	rs2267535
Chromosome Location	chr3:42557199-42557200
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:42556101..42557803-chr3:42559500..42561568,2	K562	blood:
2	chr3:42555090..42557381-chr3:42567941..42570291,2	MCF-7	breast:
3	chr3:42543941..42547920-chr3:42554474..42558044,4	K562	blood:

Variant related genes	Relation type
ENSG00000114812	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs12493238	0.82[ASN][1000 genomes]
rs12493291	0.83[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs2239499	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2239500	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2267534	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2267536	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2267537	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2267538	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2284132	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28684623	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs407931	0.83[CHB][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap]
rs414977	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs450812	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs58526597	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs735773	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7625494	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7635291	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7640893	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs811198	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9841214	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529987	chr3:41921995-42591771	Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv1005533	chr3:41953873-42596375	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	esv1804804	chr3:42515186-42582403	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv527430	chr3:42534042-42557199	Weak transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	esv1814102	chr3:42539966-42582403	Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	esv3439679	chr3:42555248-42559546	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2267535	VIPR1	cis	cerebellum	SCAN

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42547200-42561800	Genic enhancers	Fetal Intestine Small	intestine
2	chr3:42547600-42579000	Weak transcription	Rectal Smooth Muscle	rectum
3	chr3:42549200-42561800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr3:42549800-42560600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr3:42550000-42560400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr3:42550200-42558200	Enhancers	Right Ventricle	heart
7	chr3:42550600-42558800	Enhancers	Right Atrium	heart
8	chr3:42551200-42559200	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr3:42551400-42558800	Enhancers	Left Ventricle	heart
10	chr3:42552200-42581000	Weak transcription	Pancreas	Pancrea
11	chr3:42552400-42558400	Genic enhancers	Rectal Mucosa Donor 31	rectum
12	chr3:42552400-42570000	Weak transcription	Fetal Stomach	stomach
13	chr3:42553200-42560800	Weak transcription	Small Intestine	intestine
14	chr3:42553600-42559000	Genic enhancers	Lung	lung
15	chr3:42553600-42566600	Weak transcription	Primary B cells from cord blood	blood
16	chr3:42553800-42560400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr3:42554000-42557800	Weak transcription	Placenta	Placenta
18	chr3:42554000-42559000	Strong transcription	Primary T cells from cord blood	blood
19	chr3:42554000-42560200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr3:42554400-42558600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr3:42554600-42559000	Enhancers	Stomach Mucosa	stomach
22	chr3:42554800-42559200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr3:42555000-42557400	Weak transcription	Adipose Nuclei	Adipose
24	chr3:42555600-42557600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
25	chr3:42555600-42559200	Enhancers	Fetal Heart	heart
26	chr3:42555800-42559200	Enhancers	Esophagus	oesophagus
27	chr3:42555800-42560600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr3:42556000-42557400	Enhancers	Brain Anterior Caudate	brain
29	chr3:42556000-42558000	Enhancers	Brain Inferior Temporal Lobe	brain
30	chr3:42556000-42558200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr3:42556200-42557600	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
32	chr3:42556200-42557600	Enhancers	Brain Cingulate Gyrus	brain
33	chr3:42556200-42557800	Enhancers	Brain Substantia Nigra	brain
34	chr3:42556200-42557800	Enhancers	Skeletal Muscle Male	skeletal muscle
35	chr3:42556200-42558000	Enhancers	Brain Hippocampus Middle	brain
36	chr3:42556200-42558400	Genic enhancers	Spleen	Spleen
37	chr3:42556200-42559000	Genic enhancers	Fetal Intestine Large	intestine
38	chr3:42556400-42557200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr3:42556400-42557600	Enhancers	Brain Angular Gyrus	brain
40	chr3:42556400-42557800	Enhancers	Aorta	Aorta
41	chr3:42556400-42558000	Enhancers	Skeletal Muscle Female	skeletal muscle
42	chr3:42556400-42558800	Enhancers	Gastric	stomach
43	chr3:42556400-42559400	Enhancers	Colonic Mucosa	Colon
44	chr3:42556600-42557400	Enhancers	Duodenum Mucosa	Duodenum
45	chr3:42556600-42557600	Flanking Active TSS	HMEC	breast
46	chr3:42556800-42557200	Enhancers	Cortex derived primary cultured neurospheres	brain
47	chr3:42556800-42557600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr3:42556800-42558400	Enhancers	Rectal Mucosa Donor 29	rectum
49	chr3:42556800-42560200	Weak transcription	Primary T helper cells fromperipheralblood	blood
50	chr3:42556800-42560200	Strong transcription	Monocytes-CD14+_RO01746	blood

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