Variant report

Variant	rs10119731
Chromosome Location	chr9:16792350-16792351
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10115109	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10116407	0.91[TSI][hapmap]
rs10119811	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10120562	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10121347	1.00[CEU][hapmap];0.85[GIH][hapmap];0.89[MEX][hapmap];0.84[EUR][1000 genomes]
rs10122901	0.89[EUR][1000 genomes]
rs10123118	0.91[TSI][hapmap]
rs10125996	1.00[CEU][hapmap];0.81[CHB][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10810622	0.83[CHB][hapmap]
rs10962576	0.91[TSI][hapmap]
rs10962588	0.83[CHB][hapmap]
rs10962592	1.00[TSI][hapmap];0.80[EUR][1000 genomes]
rs10962601	1.00[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10962609	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs12338608	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12341168	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12341542	0.92[GIH][hapmap];0.89[MEX][hapmap]
rs12351269	1.00[CEU][hapmap];0.96[GIH][hapmap];0.89[MEX][hapmap];0.84[EUR][1000 genomes]
rs12376135	0.91[EUR][1000 genomes]
rs12378588	0.81[AMR][1000 genomes]
rs12380481	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16935073	0.96[GIH][hapmap]
rs1856132	0.91[TSI][hapmap]
rs2039185	0.83[CHB][hapmap]
rs2150089	0.82[TSI][hapmap]
rs2183406	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2183407	1.00[CEU][hapmap];0.85[CHB][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2253579	0.88[CEU][hapmap];0.89[GIH][hapmap];0.84[JPT][hapmap];0.88[MEX][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28584140	0.80[EUR][1000 genomes]
rs4455968	0.85[EUR][1000 genomes]
rs7861591	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530933	chr9:16251206-16830845	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1024799	chr9:16631890-17431827	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	esv2758627	chr9:16641966-16809203	Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	esv2759673	chr9:16641966-16809203	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv892650	chr9:16696187-16950860	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv613671	chr9:16792350-16804082	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10119731	BCAS3	trans	lymphoblastoid	seeQTL
rs10119731	CHL1	trans	lymphoblastoid	seeQTL

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:16767600-16795400	Weak transcription	Fetal Muscle Leg	muscle
2	chr9:16768000-16795000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr9:16769800-16795400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr9:16773000-16795000	Weak transcription	HSMMtube	muscle
5	chr9:16784400-16802200	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr9:16785200-16794600	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr9:16786000-16795600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr9:16787000-16792400	Weak transcription	Colon Smooth Muscle	Colon
9	chr9:16787000-16794600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr9:16787000-16795200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr9:16787200-16794800	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr9:16787200-16797600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr9:16787600-16792600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr9:16787600-16795000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr9:16788000-16795000	Weak transcription	Fetal Stomach	stomach
16	chr9:16788200-16794400	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr9:16788200-16794600	Weak transcription	NHDF-Ad	bronchial
18	chr9:16788200-16794800	Weak transcription	HSMM	muscle
19	chr9:16788200-16795000	Weak transcription	NHLF	lung
20	chr9:16788200-16798000	Weak transcription	Stomach Smooth Muscle	stomach
21	chr9:16789000-16794200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr9:16790400-16793800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr9:16791800-16792600	Enhancers	Ovary	ovary
24	chr9:16792000-16794600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr9:16792200-16792600	Enhancers	iPS-18 Cell Line	embryonic stem cell
26	chr9:16792200-16793600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr9:16792200-16793600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr9:16792200-16794000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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