Variant report

Variant	rs6942223
Chromosome Location	chr6:86073267-86073268
allele	A/C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 82 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs1026064	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1028637	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10498953	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10498954	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11758883	0.84[ASN][1000 genomes]
rs1322399	0.84[ASN][1000 genomes]
rs1322400	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1322407	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1322408	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1322410	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1407446	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1575309	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17216936	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17216964	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17217290	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17217313	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17217341	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17816793	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1853254	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2181188	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2208726	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2208727	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28820930	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4337908	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4706233	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4707192	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4707193	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4707196	0.85[ASN][1000 genomes]
rs4707197	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5019880	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs5019881	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs5019882	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs5019883	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs5019884	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56305244	0.87[ASN][1000 genomes]
rs56679761	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs57115758	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs57214768	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs57393053	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs57464713	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57915056	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs58387111	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs58873354	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs59797978	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs59825200	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60034184	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs60308797	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs60696184	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60968245	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61200746	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61536412	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61620438	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62420143	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62420144	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62420145	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62444622	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62444623	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62444624	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62444625	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62444626	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62444627	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62444629	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62444632	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6930866	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6938795	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7740378	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7744735	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9344512	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9362197	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs950030	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9689843	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs969918	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs970568	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs970569	0.87[AMR][1000 genomes];0.89[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
rs6942223	MESDC2	trans	lymphoblastoid	RTeQTL
rs6942223	SNHG5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:23 , 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	chr6:86071600-86073400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr6:86071800-86074000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr6:86071800-86074000	Weak transcription	HSMM	muscle
9	chr6:86071800-86074400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr6:86072200-86073400	Enhancers	A549	lung
11	chr6:86072600-86074200	Weak transcription	Placenta	Placenta
12	chr6:86072800-86073800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr6:86072800-86073800	Weak transcription	NH-A	brain
14	chr6:86073000-86074000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr6:86073000-86074000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr6:86073000-86074000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr6:86073200-86073600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr6:86073200-86073600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr6:86073200-86073600	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr6:86073200-86073600	Weak transcription	Hela-S3	cervix
21	chr6:86073200-86073600	Weak transcription	HMEC	breast
22	chr6:86073200-86073600	Weak transcription	HUVEC	blood vessel
23	chr6:86073200-86073600	Weak transcription	NHEK	skin

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