Variant report

Variant	rs7962334
Chromosome Location	chr12:32964505-32964506
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:32962332..32964865-chr12:32975900..32977825,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000057294	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10844364	0.83[EUR][1000 genomes]
rs10844366	0.82[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs11052256	0.94[CEU][hapmap];0.83[EUR][1000 genomes]
rs1114701	0.84[MEX][hapmap]
rs1114702	0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs1823924	0.82[AMR][1000 genomes]
rs2022140	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2389107	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4931044	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4931045	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6488090	0.86[JPT][hapmap]
rs6488095	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6488097	0.80[MEX][hapmap];0.87[TSI][hapmap]
rs7303077	1.00[CHB][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7308045	0.90[CHB][hapmap];0.85[JPT][hapmap];0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]

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	nsv530421	chr12:32825335-33465991	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv1054440	chr12:32872999-33150460	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv532334	chr12:32884789-33034791	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	esv3409346	chr12:32962935-32964933	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	esv2485280	chr12:32963502-32965564	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7962334	CAPRIN2	cis	cerebellum	SCAN

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:32941800-33033400	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr12:32943800-33026800	Weak transcription	Fetal Kidney	kidney
3	chr12:32944200-32989400	Weak transcription	Hela-S3	cervix
4	chr12:32945800-32972400	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr12:32946000-32973600	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr12:32946600-32967200	Weak transcription	Stomach Mucosa	stomach
7	chr12:32949200-32975200	Weak transcription	Stomach Smooth Muscle	stomach
8	chr12:32949200-32987000	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr12:32949200-33007800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr12:32954400-32968800	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr12:32959000-32965000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr12:32960200-32969200	Weak transcription	Small Intestine	intestine
13	chr12:32960800-32965400	Strong transcription	Rectal Mucosa Donor 29	rectum
14	chr12:32961000-32989800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr12:32961400-32965200	Strong transcription	Duodenum Mucosa	Duodenum
16	chr12:32961400-32969400	Strong transcription	NHEK	skin
17	chr12:32961400-32971000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr12:32961600-32965200	Strong transcription	Rectal Mucosa Donor 31	rectum
19	chr12:32961800-32973400	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr12:32961800-32974800	Weak transcription	Rectal Smooth Muscle	rectum
21	chr12:32962000-32965000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr12:32962000-32965400	Strong transcription	Liver	Liver
23	chr12:32962000-32973600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr12:32962200-32965400	Enhancers	Brain Cingulate Gyrus	brain
25	chr12:32962200-32969200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr12:32962200-32974000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr12:32962400-32964600	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr12:32962400-32970600	Weak transcription	Fetal Stomach	stomach
29	chr12:32962400-32973400	Weak transcription	Gastric	stomach
30	chr12:32962400-32973400	Weak transcription	Right Atrium	heart
31	chr12:32962600-32965000	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr12:32962600-32965000	Enhancers	Brain Hippocampus Middle	brain
33	chr12:32962600-32973400	Weak transcription	Pancreas	Pancrea
34	chr12:32962800-32967000	Weak transcription	Right Ventricle	heart
35	chr12:32963000-32968200	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr12:32963000-32970600	Weak transcription	Fetal Intestine Small	intestine
37	chr12:32963000-32986800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr12:32963200-32967000	Weak transcription	Placenta	Placenta
39	chr12:32963400-32964600	Strong transcription	HMEC	breast
40	chr12:32963400-32968800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr12:32963600-32964800	Weak transcription	HSMMtube	muscle
42	chr12:32963800-32965000	Strong transcription	HepG2	liver
43	chr12:32963800-32965400	Strong transcription	Sigmoid Colon	Sigmoid Colon
44	chr12:32964000-32964600	Enhancers	Brain Angular Gyrus	brain
45	chr12:32964000-32965000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr12:32964000-32965200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr12:32964200-32965000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr12:32964400-32964800	Flanking Active TSS	Fetal Heart	heart
49	chr12:32964400-32969000	Weak transcription	Fetal Intestine Large	intestine
50	chr12:32964400-32970600	Weak transcription	Left Ventricle	heart

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