Variant report

Variant	rs211717
Chromosome Location	chr1:76106969-76106970
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:76094932..76097642-chr1:76105459..76107452,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLC44A5-4	chr1:76105925-76108177	NONHSAT003984

Extended variants
information (count: 69 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10873685	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11161437	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11161468	0.80[EUR][1000 genomes]
rs11161511	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11163924	0.82[AFR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12091720	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12123977	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12126607	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12127402	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12134854	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1498312	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1498315	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1498316	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1498317	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17587071	0.81[EUR][1000 genomes]
rs1855136	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1858536	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1890451	0.82[EUR][1000 genomes]
rs2066183	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs211718	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs211737	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs380075	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs392691	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4559448	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4646961	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4949674	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4949872	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4949874	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4949875	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4949876	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4949877	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs60378926	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61622554	0.81[EUR][1000 genomes]
rs61797339	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs6593585	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6688749	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7513363	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7513559	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7515955	0.83[ASN][1000 genomes]
rs7516122	0.82[AFR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7518038	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7524467	0.82[EUR][1000 genomes]
rs7533888	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7534754	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7535991	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7539246	0.82[EUR][1000 genomes]
rs7544117	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7546641	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7548962	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7549167	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7552404	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs942270	0.83[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
rs211717	MSH4	cis	Artery Tibial	GTEx
rs211717	MSH4	cis	Esophagus Muscularis	GTEx
rs211717	ACADM	cis	Muscle Skeletal	GTEx
rs211717	ACADM	cis	Whole Blood	GTEx

Chromatin state (count:0 , 50 per page) page:

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dbSNP/dbVar ID: rs12345 /nsv7879
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