Variant report

Variant	rs2029683
Chromosome Location	chr1:76341643-76341644
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:76256252..76258786-chr1:76340738..76342721,2	K562	blood:

Variant related genes	Relation type
ENSG00000137955	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10732723	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs10873787	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10873788	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10873808	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10873863	0.81[CEU][hapmap]
rs11161620	0.83[CEU][hapmap];1.00[CHB][hapmap];0.80[EUR][1000 genomes]
rs11161626	0.80[EUR][1000 genomes]
rs11161792	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11161836	1.00[CEU][hapmap]
rs11161845	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161857	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs1144336	0.82[EUR][1000 genomes]
rs1146646	1.00[CHB][hapmap]
rs1146653	0.82[EUR][1000 genomes]
rs11588578	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs1159214	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs12021855	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12090849	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs12093623	0.84[CEU][hapmap];1.00[CHB][hapmap];0.80[EUR][1000 genomes]
rs12118399	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12122939	0.83[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs12127078	0.80[EUR][1000 genomes]
rs12136360	0.83[EUR][1000 genomes]
rs12568447	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12723575	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1417405	1.00[ASN][1000 genomes]
rs1565717	0.87[CEU][hapmap];1.00[CHB][hapmap];0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1689275	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17650138	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1770885	0.95[CEU][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1770887	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2029681	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2172507	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2172508	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2347962	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2881786	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4949677	0.81[CEU][hapmap];0.80[EUR][1000 genomes]
rs4949683	1.00[ASN][1000 genomes]
rs4949686	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs4949885	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs5745336	0.84[CEU][hapmap];1.00[CHB][hapmap];0.80[EUR][1000 genomes]
rs5745363	0.81[EUR][1000 genomes]
rs5745381	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs5745390	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs5745427	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs5745433	0.87[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs5745442	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs5745449	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs61770533	0.82[EUR][1000 genomes]
rs61770550	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61770556	1.00[ASN][1000 genomes]
rs61770557	1.00[ASN][1000 genomes]
rs6678348	0.84[EUR][1000 genomes]
rs6683437	0.88[CEU][hapmap];1.00[CHB][hapmap]
rs6699682	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs7523573	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs7538800	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7547056	0.83[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs7549863	1.00[CHB][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs931507	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv1004669	chr1:76301198-76409451	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv871671	chr1:76304215-76391646	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2029683	MSH4	cis	Artery Tibial	GTEx
rs2029683	MSH4	cis	Esophagus Muscularis	GTEx
rs2029683	MAZ	trans	lymphoblastoid	RTeQTL
rs2029683	MSH4	cis	Nerve Tibial	GTEx

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

No data

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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