Variant report

Variant	rs7515955
Chromosome Location	chr1:76143884-76143885
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:76140961..76144068-chr1:76250261..76252961,3	K562	blood:
2	chr1:76138718..76140997-chr1:76142345..76144918,2	K562	blood:

Variant related genes	Relation type
ENSG00000206620	Chromatin interaction
ENSG00000137955	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs11161493	0.83[EUR][1000 genomes]
rs11163924	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1146574	0.82[EUR][1000 genomes]
rs1146579	0.82[EUR][1000 genomes]
rs1146580	0.82[EUR][1000 genomes]
rs1146581	0.82[EUR][1000 genomes]
rs1146588	0.81[EUR][1000 genomes]
rs12134854	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12136754	0.82[EUR][1000 genomes]
rs1250874	0.82[EUR][1000 genomes]
rs1251075	0.82[EUR][1000 genomes]
rs1303169	0.80[EUR][1000 genomes]
rs1313071	0.81[EUR][1000 genomes]
rs1498312	0.81[EUR][1000 genomes]
rs1498315	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1498316	0.83[ASN][1000 genomes]
rs1498317	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1611823	0.82[EUR][1000 genomes]
rs1612097	0.82[EUR][1000 genomes]
rs1694419	0.82[EUR][1000 genomes]
rs1767456	0.82[EUR][1000 genomes]
rs1767458	0.82[EUR][1000 genomes]
rs1770511	0.81[EUR][1000 genomes]
rs1855136	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1858536	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1890452	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2066183	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs211717	0.83[ASN][1000 genomes]
rs211718	0.83[ASN][1000 genomes]
rs211737	0.83[ASN][1000 genomes]
rs2153126	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2173378	0.82[EUR][1000 genomes]
rs2185435	0.83[EUR][1000 genomes]
rs2185436	0.83[EUR][1000 genomes]
rs2275378	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2788654	0.82[EUR][1000 genomes]
rs3818855	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs392691	0.83[ASN][1000 genomes]
rs4949872	0.83[ASN][1000 genomes]
rs4949874	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4949875	0.81[EUR][1000 genomes]
rs4949876	0.83[EUR][1000 genomes]
rs57186386	0.82[EUR][1000 genomes]
rs60378926	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6593514	0.83[EUR][1000 genomes]
rs6593515	0.81[EUR][1000 genomes]
rs6593585	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6688749	0.81[EUR][1000 genomes]
rs7513363	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7513559	0.80[EUR][1000 genomes]
rs7516122	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7518038	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7533888	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7535991	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7541058	0.82[AMR][1000 genomes]
rs7544117	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7546641	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7548962	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7549167	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7550974	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7552404	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7554984	0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519329	chr1:75830438-76358591	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	esv2757737	chr1:75986904-76187748	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	esv2758943	chr1:75986904-76187748	Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv427675	chr1:76070382-76187748	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	esv2756846	chr1:76083408-76156986	Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv870520	chr1:76088392-76206490	Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv830281	chr1:76095292-76251053	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
8	nsv945914	chr1:76109781-76172388	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7515955	MSH4	cis	Artery Tibial	GTEx

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76142600-76144000	Active TSS	H1 Cell Line	embryonic stem cell
2	chr1:76142600-76144000	Active TSS	HUES48 Cell Line	embryonic stem cell
3	chr1:76142600-76144000	Active TSS	HepG2	liver
4	chr1:76143000-76144000	Active TSS	HUES6 Cell Line	embryonic stem cell
5	chr1:76143400-76144000	Active TSS	H9 Cell Line	embryonic stem cell
6	chr1:76143400-76144000	Active TSS	iPS-18 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links