Variant report

Variant	rs12344698
Chromosome Location	chr9:16750143-16750144
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10116407	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs10116469	1.00[CEU][hapmap]
rs10117034	0.80[EUR][1000 genomes]
rs10122736	0.86[CEU][hapmap]
rs10122827	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs10123118	1.00[CEU][hapmap];0.82[CHB][hapmap];0.80[EUR][1000 genomes]
rs10733320	0.92[ASN][1000 genomes]
rs10738457	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10756810	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10810595	1.00[CEU][hapmap]
rs10810599	0.89[EUR][1000 genomes]
rs10810600	0.96[EUR][1000 genomes]
rs10810602	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10810610	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs10810614	0.96[EUR][1000 genomes]
rs10810615	0.93[EUR][1000 genomes]
rs10810617	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs10810622	0.80[EUR][1000 genomes]
rs10962543	0.87[CEU][hapmap]
rs10962556	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10962569	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs10962576	1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[EUR][1000 genomes]
rs10962592	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs12238070	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12341542	1.00[CEU][hapmap]
rs12375507	0.87[CEU][hapmap]
rs12377846	0.85[CEU][hapmap]
rs1337386	0.96[EUR][1000 genomes]
rs1361073	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs1856132	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.93[JPT][hapmap];0.96[EUR][1000 genomes]
rs1999214	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2039185	1.00[CEU][hapmap]
rs2150089	1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[EUR][1000 genomes]
rs2282072	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.89[EUR][1000 genomes]
rs28584140	0.81[EUR][1000 genomes]
rs28626673	0.82[EUR][1000 genomes]
rs5016914	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7024466	0.82[CHB][hapmap]
rs73419969	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7855044	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7862734	1.00[CEU][hapmap];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv530934	chr9:16281246-16779432	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv1032856	chr9:16465330-16773471	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS 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	11 gene(s)	inside rSNPs	diseases
4	nsv540073	chr9:16465330-16773471	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh 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	11 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	nsv892649	chr9:16677221-16761597	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12344698	CXCL10	trans	brain	seeQTL
rs12344698	MT1A	trans	brain	seeQTL
rs12344698	CD93	trans	brain	seeQTL
rs12344698	FSTL1	trans	brain	seeQTL
rs12344698	THBD	trans	brain	seeQTL

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:16745400-16752400	Weak transcription	Colon Smooth Muscle	Colon
2	chr9:16745400-16758000	Weak transcription	Ovary	ovary
3	chr9:16745400-16774800	Weak transcription	Osteobl	bone
4	chr9:16745600-16750600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr9:16745600-16752200	Weak transcription	NHDF-Ad	bronchial
6	chr9:16745600-16766200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr9:16748000-16752200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr9:16748200-16752200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr9:16749000-16750600	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr9:16749000-16750800	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr9:16749600-16750200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr9:16749600-16750400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr9:16749600-16755000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr9:16750000-16755200	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr9:16750000-16756000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr9:16750000-16756600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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