Variant report

Variant	rs392691
Chromosome Location	chr1:76097044-76097045
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:76094259..76097858-chr1:76188776..76191867,4	K562	blood:
2	chr1:76096029..76098574-chr1:76101114..76103972,2	K562	blood:
3	chr1:76094932..76097642-chr1:76105459..76107452,2	K562	blood:
4	chr1:76087110..76089218-chr1:76095459..76097902,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000117054	Chromatin interaction
ENSG00000178193	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs11161437	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11161510	0.80[AMR][1000 genomes]
rs11161515	0.80[AMR][1000 genomes]
rs11161521	0.80[AMR][1000 genomes]
rs11163924	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12091720	0.89[ASN][1000 genomes]
rs12134854	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1498312	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1498315	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1498316	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1498317	0.89[ASN][1000 genomes]
rs1855136	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1858536	1.00[ASN][1000 genomes]
rs2066183	1.00[ASN][1000 genomes]
rs211717	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs211718	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs211737	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs380075	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4949872	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4949874	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4949875	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4949876	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60378926	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61799967	0.80[AMR][1000 genomes]
rs6593585	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6688749	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72686191	0.80[AMR][1000 genomes]
rs7513363	0.94[ASN][1000 genomes]
rs7513559	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7515955	0.83[ASN][1000 genomes]
rs7516122	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7518038	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7533888	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7534754	0.89[ASN][1000 genomes]
rs7535991	1.00[ASN][1000 genomes]
rs7544117	1.00[ASN][1000 genomes]
rs7546641	1.00[ASN][1000 genomes]
rs7548962	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7549167	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7552404	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs942270	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 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	esv3445096	chr1:75933216-76126980	Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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
7	nsv10295	chr1:76085406-76119292	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv997990	chr1:76086763-76121738	Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv1003742	chr1:76086763-76124052	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv998205	chr1:76086763-76125366	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	esv3692758	chr1:76088392-76126205	Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv546582	chr1:76088392-76126205	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
13	nsv546583	chr1:76088392-76134765	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
14	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
15	esv34738	chr1:76094234-76121479	Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
16	esv34562	chr1:76094234-76121738	Bivalent Enhancer Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
17	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs392691	MSH4	cis	Artery Tibial	GTEx
rs392691	ACADM	cis	lung	GTEx
rs392691	MSH4	cis	Esophagus Muscularis	GTEx
rs392691	ACADM	cis	Whole Blood	GTEx

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76096200-76098600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr1:76096400-76097600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
3	chr1:76096600-76097200	Enhancers	HepG2	liver

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