Variant report

Variant	rs9920722
Chromosome Location	chr15:49735112-49735113
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10519224	0.92[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10519225	0.92[CEU][hapmap];0.82[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10851479	0.82[JPT][hapmap]
rs11070699	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs11070706	0.82[JPT][hapmap]
rs11853969	0.84[CEU][hapmap]
rs11854557	0.84[CEU][hapmap]
rs11855798	0.92[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11858411	0.82[JPT][hapmap]
rs12050614	0.82[JPT][hapmap]
rs12148764	0.82[JPT][hapmap]
rs12232355	0.82[JPT][hapmap]
rs12591300	0.80[CEU][hapmap];0.83[EUR][1000 genomes]
rs12591659	0.83[JPT][hapmap]
rs12592508	0.81[CHB][hapmap]
rs12595692	0.82[JPT][hapmap]
rs12901929	0.92[CEU][hapmap];0.82[CHB][hapmap];0.91[EUR][1000 genomes]
rs12902960	0.81[JPT][hapmap]
rs12905203	0.85[CEU][hapmap];0.82[CHB][hapmap];0.85[EUR][1000 genomes]
rs12905477	0.85[CEU][hapmap]
rs12908624	0.83[JPT][hapmap]
rs12908635	0.83[JPT][hapmap]
rs12916839	0.82[CEU][hapmap];0.82[CHB][hapmap];0.83[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1395901	0.83[JPT][hapmap]
rs17402115	0.83[JPT][hapmap]
rs17478694	0.96[CEU][hapmap];0.82[CHB][hapmap];0.83[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17478785	0.96[CEU][hapmap];0.82[CHB][hapmap];0.83[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17479589	0.83[JPT][hapmap]
rs1874616	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs1904316	0.93[YRI][hapmap]
rs1911612	0.82[JPT][hapmap]
rs1976551	0.82[JPT][hapmap]
rs2202714	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs2899434	0.82[JPT][hapmap]
rs2899437	0.86[YRI][hapmap]
rs36023246	0.93[EUR][1000 genomes]
rs4389093	0.96[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4480740	0.82[JPT][hapmap]
rs4775806	0.85[CEU][hapmap]
rs6493372	0.82[JPT][hapmap]
rs7174135	0.83[JPT][hapmap]
rs7180168	0.85[CEU][hapmap]
rs753857	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs8031680	0.86[YRI][hapmap]
rs8032688	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1039368	chr15:49566094-49764066	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv833002	chr15:49621400-49781799	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv9263	chr15:49734435-49809465	Active TSS Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9920722	COPS2	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49716400-49737200	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr15:49721000-49736200	Weak transcription	Right Ventricle	heart
3	chr15:49730400-49744600	Weak transcription	NHLF	lung
4	chr15:49732000-49736600	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr15:49732000-49750200	Weak transcription	HSMM	muscle
6	chr15:49732200-49736200	Weak transcription	Ovary	ovary
7	chr15:49732200-49736200	Weak transcription	Stomach Smooth Muscle	stomach
8	chr15:49732400-49736800	Weak transcription	Fetal Stomach	stomach
9	chr15:49732400-49738200	Weak transcription	NHDF-Ad	bronchial
10	chr15:49732800-49741000	Weak transcription	Fetal Heart	heart
11	chr15:49733200-49735200	Enhancers	Colon Smooth Muscle	Colon
12	chr15:49733200-49741800	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr15:49733600-49735200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr15:49733800-49736200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr15:49734400-49735200	Enhancers	iPS-18 Cell Line	embryonic stem cell
16	chr15:49734400-49736400	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr15:49734600-49735200	Enhancers	HUES6 Cell Line	embryonic stem cell
18	chr15:49734600-49735200	Enhancers	iPS-15b Cell Line	embryonic stem cell
19	chr15:49734600-49735400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr15:49734800-49735200	Enhancers	Rectal Smooth Muscle	rectum
21	chr15:49734800-49736600	Weak transcription	Osteobl	bone

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