Variant report

Variant	rs11161688
Chromosome Location	chr1:76292520-76292521
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10873727	0.82[AFR][1000 genomes]
rs10873728	0.82[AFR][1000 genomes]
rs10873729	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10873733	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10873739	0.82[AFR][1000 genomes]
rs11161598	0.81[EUR][1000 genomes]
rs11161718	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1144338	0.82[AFR][1000 genomes]
rs1144340	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1146617	0.82[EUR][1000 genomes]
rs1146631	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1146632	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1146634	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1146636	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1146637	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1146643	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1146644	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1146656	0.80[AFR][1000 genomes]
rs11579355	0.80[AFR][1000 genomes]
rs12076093	0.82[AFR][1000 genomes]
rs12078151	0.82[AFR][1000 genomes]
rs12090712	0.82[AFR][1000 genomes]
rs12092388	0.81[EUR][1000 genomes]
rs12385715	0.80[AFR][1000 genomes]
rs12405178	0.80[AFR][1000 genomes]
rs1251272	0.82[AFR][1000 genomes]
rs1251275	0.85[AFR][1000 genomes]
rs12734931	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34045364	0.80[AFR][1000 genomes]
rs34177389	0.80[AFR][1000 genomes]
rs35591768	0.80[AFR][1000 genomes]
rs4949884	0.81[AFR][1000 genomes]
rs5019550	0.82[AFR][1000 genomes]
rs56350137	0.80[AFR][1000 genomes]
rs5745323	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7548391	0.80[AFR][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11161688	MSH4	cis	Esophagus Muscularis	GTEx
rs11161688	MSH4	cis	Muscle Skeletal	GTEx
rs11161688	RABGGTB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76262600-76294600	Weak transcription	Primary B cells from cord blood	blood
2	chr1:76263000-76296200	Weak transcription	Ovary	ovary
3	chr1:76282200-76295200	Weak transcription	Right Ventricle	heart
4	chr1:76289400-76295200	Weak transcription	Skeletal Muscle Female	skeletal muscle

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