Variant report

Variant	rs10782558
Chromosome Location	chr1:76298719-76298720
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11161620	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11161626	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161792	0.86[EUR][1000 genomes]
rs1144336	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1146646	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1146653	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12021855	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12093623	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12122939	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12127078	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12136360	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12568447	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12723575	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1565717	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2029681	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2172507	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2172508	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2347962	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2881786	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4949677	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4949885	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5745336	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5745363	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5745381	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs5745390	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs5745427	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs5745433	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61770533	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6678348	0.82[EUR][1000 genomes]
rs7538800	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7547056	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7549863	0.83[AMR][1000 genomes];0.86[EUR][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	nsv1014072	chr1:76200531-76460726	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv535005	chr1:76200531-76460726	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	esv1795237	chr1:76268573-76383565	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	esv1800125	chr1:76269439-76379497	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	esv1799260	chr1:76269439-76383297	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	esv1847721	chr1:76269439-76383565	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1466	chr1:76280957-76299478	ZNF genes & repeats Weak transcription Enhancers Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10782558	MSH4	cis	Esophagus Muscularis	GTEx
rs10782558	MSH4	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76295800-76307800	Weak transcription	Skeletal Muscle Female	skeletal muscle

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