Variant report

Variant	rs591895
Chromosome Location	chr7:26887112-26887113
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10257437	0.87[CEU][hapmap]
rs10257464	0.87[CEU][hapmap]
rs10259208	0.85[CEU][hapmap]
rs11973332	0.81[TSI][hapmap]
rs11976472	0.82[MEX][hapmap];0.81[TSI][hapmap]
rs1391805	0.83[YRI][hapmap]
rs213515	0.94[CEU][hapmap]
rs213516	0.87[CEU][hapmap]
rs213525	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs213528	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs213533	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs213536	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2140998	0.81[CEU][hapmap]
rs471536	1.00[JPT][hapmap]
rs477924	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs490366	0.83[YRI][hapmap]
rs514043	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs550141	0.83[YRI][hapmap]
rs558263	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs564260	1.00[JPT][hapmap]
rs586947	0.96[YRI][hapmap];0.87[AFR][1000 genomes]
rs640512	1.00[JPT][hapmap]
rs659131	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs668052	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs673502	1.00[JPT][hapmap]
rs688039	1.00[JPT][hapmap]
rs6967749	0.82[MEX][hapmap];0.81[TSI][hapmap]
rs774252	0.87[CEU][hapmap]
rs774265	0.94[CEU][hapmap];0.81[GIH][hapmap]
rs7791056	0.87[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025538	chr7:26482342-27376045	Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
2	nsv538805	chr7:26482342-27376045	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs591895	CBX3	cis	parietal	SCAN
rs591895	HOXA2	Cis_1M	lymphoblastoid	RTeQTL
rs591895	STK31	cis	cerebellum	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:26863200-26893200	Weak transcription	A549	lung
2	chr7:26863600-26894600	Weak transcription	Fetal Intestine Large	intestine
3	chr7:26867200-26897000	Weak transcription	Lung	lung
4	chr7:26869200-26889800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr7:26870400-26894400	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr7:26870600-26896000	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr7:26871000-26902200	Weak transcription	Dnd41	blood
8	chr7:26871600-26896000	Weak transcription	Rectal Smooth Muscle	rectum
9	chr7:26872400-26896200	Weak transcription	Fetal Intestine Small	intestine
10	chr7:26872600-26890000	Weak transcription	NHEK	skin
11	chr7:26872600-26894800	Weak transcription	Primary hematopoietic stem cells	blood
12	chr7:26872800-26892800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr7:26875200-26889600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr7:26875600-26896000	Weak transcription	Stomach Smooth Muscle	stomach
15	chr7:26876000-26896000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr7:26876200-26896200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr7:26876600-26889800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr7:26877200-26894400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr7:26877200-26897000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr7:26877200-26897000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr7:26877400-26892600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr7:26877400-26893600	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr7:26878000-26892800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr7:26878600-26889800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr7:26878800-26893200	Weak transcription	NHLF	lung
26	chr7:26881200-26890800	Weak transcription	Liver	Liver
27	chr7:26881200-26892800	Weak transcription	HMEC	breast
28	chr7:26883000-26890200	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr7:26883200-26889800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr7:26883200-26893400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr7:26883200-26895800	Weak transcription	Adipose Nuclei	Adipose
32	chr7:26883800-26894800	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr7:26883800-26896000	Weak transcription	NHDF-Ad	bronchial
34	chr7:26884000-26889600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr7:26884200-26893400	Weak transcription	HUVEC	blood vessel
36	chr7:26884800-26889600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr7:26884800-26893600	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr7:26885200-26887800	Strong transcription	Primary neutrophils fromperipheralblood	blood
39	chr7:26886200-26903400	Weak transcription	Spleen	Spleen
40	chr7:26886600-26893000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr7:26886800-26888800	Strong transcription	Primary B cells from cord blood	blood
42	chr7:26886800-26888800	Strong transcription	Primary B cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links