Variant report

Variant	rs596463
Chromosome Location	chr2:234952319-234952320
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	2:234635414-234639782..2:234945222-234954947	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000243135	Chromatin interaction
ENSG00000241635	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10168712	0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs10171587	0.95[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs10172000	0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs10193392	0.95[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.99[ASN][1000 genomes]
rs10197450	0.81[JPT][hapmap]
rs10200368	0.95[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10205160	0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs10207367	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1354895	0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs1354896	0.96[ASN][1000 genomes]
rs17866614	0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs17866615	0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs1911592	0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs1911593	0.95[ASN][1000 genomes]
rs1911594	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.95[ASN][1000 genomes]
rs2267900	0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs2267902	0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs2267903	0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs2267904	0.96[ASN][1000 genomes]
rs2284293	0.80[AMR][1000 genomes]
rs3771331	0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs4233639	0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs4664007	0.95[ASN][1000 genomes]
rs620654	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs622060	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs634613	0.95[GIH][hapmap];0.82[MEX][hapmap];0.84[EUR][1000 genomes]
rs665535	0.84[EUR][1000 genomes]
rs6739495	0.96[ASN][1000 genomes]
rs7603271	0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs7608191	0.95[ASN][1000 genomes]
rs9636246	0.84[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013712	chr2:234558457-235495825	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv532476	chr2:234595695-235134381	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv834571	chr2:234929288-235110332	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv2760543	chr2:234938082-234955890	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	n/a
5	nsv1006508	chr2:234938781-234955878	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	n/a
6	nsv437316	chr2:234939481-234956344	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	n/a
7	nsv1003303	chr2:234940575-234955878	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	n/a
8	nsv1000752	chr2:234941290-234955878	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	n/a
9	nsv1006053	chr2:234941290-234963441	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	n/a
10	nsv1007335	chr2:234941290-234964316	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	n/a
11	nsv517003	chr2:234942723-234953978	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
12	esv3692765	chr2:234942723-234954619	Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	n/a
13	nsv584712	chr2:234942723-234954619	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	n/a
14	esv1794753	chr2:234943285-234954902	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	n/a
15	nsv999819	chr2:234943285-234955719	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	n/a
16	nsv1002828	chr2:234943285-234955878	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	n/a
17	nsv1001846	chr2:234943285-234963541	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	n/a
18	nsv1014499	chr2:234943592-234955878	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs596463	TRIP12	cis	cerebellum	SCAN
rs596463	GPR55	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234941800-234952600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:234947400-234952600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr2:234952000-234953000	Enhancers	HMEC	breast
4	chr2:234952200-234953600	Enhancers	A549	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links