Variant report

Variant	rs10772008
Chromosome Location	chr12:32974245-32974246
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10743803	0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10844364	0.91[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11052256	0.85[CHB][hapmap];0.92[CHD][hapmap];0.88[GIH][hapmap];0.91[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11052259	0.90[CHB][hapmap];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11052262	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1114701	0.85[CHB][hapmap];0.90[CHD][hapmap];0.88[MEX][hapmap];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12821727	0.87[ASN][1000 genomes]
rs1840396	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1902140	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2124152	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2389108	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2892685	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4272862	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4931047	0.82[CHD][hapmap]
rs6488097	0.80[CHB][hapmap];0.82[CHD][hapmap];0.84[MEX][hapmap];0.81[AMR][1000 genomes]
rs7138966	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7303077	0.86[CEU][hapmap]
rs7308045	0.93[CEU][hapmap]
rs7314621	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7975824	0.90[ASN][1000 genomes]

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	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	nsv531961	chr12:32966192-32997952	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10772008	CAPRIN2	cis	cerebellum	SCAN

Chromatin state (count:55 , 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	chr12:32949200-32975200	Weak transcription	Stomach Smooth Muscle	stomach
5	chr12:32949200-32987000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr12:32949200-33007800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr12:32961000-32989800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr12:32961800-32974800	Weak transcription	Rectal Smooth Muscle	rectum
9	chr12:32963000-32986800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr12:32965000-32977800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr12:32965000-32996200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr12:32966600-32977800	Strong transcription	Duodenum Mucosa	Duodenum
13	chr12:32967000-32977800	Strong transcription	Rectal Mucosa Donor 31	rectum
14	chr12:32967000-32979000	Strong transcription	Rectal Mucosa Donor 29	rectum
15	chr12:32968400-32977400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
16	chr12:32970400-32977600	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr12:32970600-32975200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr12:32970800-32978600	Weak transcription	Small Intestine	intestine
19	chr12:32971200-32981400	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr12:32971400-32976600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr12:32972000-33029000	Weak transcription	Primary hematopoietic stem cells	blood
22	chr12:32972400-32977600	Strong transcription	HUES6 Cell Line	embryonic stem cell
23	chr12:32972600-32974600	Strong transcription	Sigmoid Colon	Sigmoid Colon
24	chr12:32972600-32975000	Strong transcription	NHEK	skin
25	chr12:32972600-32977600	Strong transcription	Primary neutrophils fromperipheralblood	blood
26	chr12:32972600-32977600	Strong transcription	Fetal Intestine Large	intestine
27	chr12:32972600-32978600	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr12:32972800-32974800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr12:32972800-32977600	Strong transcription	HepG2	liver
30	chr12:32973000-32976400	Strong transcription	Liver	Liver
31	chr12:32973000-32989600	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr12:32973200-32976200	Enhancers	Placenta Amnion	Placenta Amnion
33	chr12:32973400-32974400	Strong transcription	Pancreas	Pancrea
34	chr12:32973400-32974400	Active TSS	Right Atrium	heart
35	chr12:32973400-32974600	Strong transcription	Colonic Mucosa	Colon
36	chr12:32973400-32974600	Strong transcription	Gastric	stomach
37	chr12:32973400-32975800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr12:32973400-32976000	Strong transcription	HUES48 Cell Line	embryonic stem cell
39	chr12:32973400-32976200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr12:32973600-32974400	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr12:32973600-32974600	Strong transcription	H1 Cell Line	embryonic stem cell
42	chr12:32973600-32974600	Strong transcription	Fetal Intestine Small	intestine
43	chr12:32973600-32974600	Strong transcription	Fetal Stomach	stomach
44	chr12:32973600-32975000	Enhancers	HSMMtube	muscle
45	chr12:32973600-32975800	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr12:32974000-32974600	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr12:32974000-32976000	Genic enhancers	HMEC	breast
48	chr12:32974000-32980800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
49	chr12:32974000-32987000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr12:32974200-32974400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links