Variant report

Variant	rs4707197
Chromosome Location	chr6:86074096-86074097
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 85 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs1026064	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1028637	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10498953	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10498954	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11758883	0.84[ASN][1000 genomes]
rs1322399	0.84[ASN][1000 genomes]
rs1322400	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1322407	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1322408	0.91[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1322409	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs1322410	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1407446	0.90[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1575309	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17216936	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17216964	0.91[CEU][hapmap];0.83[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17217290	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17217313	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17217341	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17816793	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1853254	0.91[CEU][hapmap];0.80[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2181188	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2208726	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2208727	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28820930	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4337908	0.91[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4706233	0.81[CHB][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4707192	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4707193	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4707196	0.85[ASN][1000 genomes]
rs5019880	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs5019881	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs5019882	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs5019883	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs5019884	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56305244	0.87[ASN][1000 genomes]
rs56679761	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs57115758	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs57214768	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs57393053	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs57464713	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57915056	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs58387111	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs58873354	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs59797978	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs59825200	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60034184	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs60308797	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs60696184	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60968245	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61200746	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61536412	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61620438	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62420143	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62420144	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62420145	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62444622	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62444623	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62444624	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62444625	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62444626	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62444627	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62444629	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62444632	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6908264	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs6930866	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6938795	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6942223	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7740378	0.90[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7744735	0.80[CHB][hapmap];0.89[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7745109	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs9344512	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9362197	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs950030	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9689843	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs969918	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs970568	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs970569	0.86[AMR][1000 genomes];0.90[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	nsv1017418	chr6:85344786-86259540	Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Enhancers Bivalent/Poised TSS Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv538347	chr6:85344786-86259540	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv1022445	chr6:85972678-86392968	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
4	nsv538349	chr6:85972678-86392968	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
5	nsv830721	chr6:85987644-86147414	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	esv3326486	chr6:86020165-86292456	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv1019960	chr6:86023236-86136666	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	esv3435075	chr6:86052235-86271910	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4707197	MESDC2	trans	lymphoblastoid	RTeQTL
rs4707197	SNHG5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:86067600-86074400	Enhancers	NHDF-Ad	bronchial
2	chr6:86067800-86074400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr6:86069000-86074400	Enhancers	NHLF	lung
4	chr6:86069200-86074200	Enhancers	Osteobl	bone
5	chr6:86069200-86074400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr6:86071800-86074400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr6:86072600-86074200	Weak transcription	Placenta	Placenta
8	chr6:86073600-86074400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr6:86073600-86074400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr6:86073600-86074400	Enhancers	Muscle Satellite Cultured Cells	--
11	chr6:86073600-86074400	Enhancers	Hela-S3	cervix
12	chr6:86073600-86074400	Enhancers	HMEC	breast
13	chr6:86073600-86074400	Enhancers	HUVEC	blood vessel
14	chr6:86073600-86074400	Enhancers	NHEK	skin
15	chr6:86073800-86074200	Enhancers	A549	lung
16	chr6:86073800-86074400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr6:86073800-86074400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr6:86073800-86074400	Enhancers	NH-A	brain
19	chr6:86074000-86074400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr6:86074000-86074400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr6:86074000-86074400	Enhancers	HSMM	muscle

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