Variant report

Variant	rs413382
Chromosome Location	chr9:6142948-6142949
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 74 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10739084	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11793956	1.00[CHB][hapmap]
rs1330124	1.00[CHD][hapmap];0.88[GIH][hapmap];0.83[TSI][hapmap]
rs1332291	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1332292	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1537285	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1556470	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1591044	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs168168	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1755531	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1970089	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2150969	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs340887	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs340893	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs340894	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs340896	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs340901	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs340902	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs340903	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs340904	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs340905	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs340906	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs340918	0.87[EUR][1000 genomes]
rs340919	0.87[EUR][1000 genomes]
rs340921	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs340922	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs340923	0.87[EUR][1000 genomes]
rs340924	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs340925	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs340926	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs340933	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs369996	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs371165	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs371454	0.81[EUR][1000 genomes]
rs372560	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs374672	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs375560	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs376690	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs380568	1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap]
rs380888	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs390158	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs394879	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs397916	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs398561	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs399834	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs401731	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs401834	0.81[EUR][1000 genomes]
rs420445	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs425489	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs437389	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs441616	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs442851	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs443175	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs503384	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs503507	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs531759	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs639247	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs694796	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs695013	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7850455	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs821164	0.87[EUR][1000 genomes]
rs9407312	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9407324	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9408638	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs974936	0.86[AMR][1000 genomes];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	nsv948847	chr9:5712626-6417677	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv1031086	chr9:5806949-6630686	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv539967	chr9:5806949-6630686	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	nsv613205	chr9:6032924-6332901	Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv916394	chr9:6055497-6322471	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv892157	chr9:6093790-6322415	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv933124	chr9:6099101-6644738	Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
8	nsv831496	chr9:6101763-6285088	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv521598	chr9:6142157-6291125	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs413382	JAK2	cis	cerebellum	SCAN
rs413382	SMARCA2	cis	parietal	SCAN
rs413382	KDM4C	cis	lymphoblastoid	seeQTL

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:6135600-6152800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr9:6142200-6144000	Enhancers	Stomach Mucosa	stomach
3	chr9:6142600-6143000	Flanking Active TSS	Liver	Liver
4	chr9:6142600-6143000	Enhancers	Gastric	stomach
5	chr9:6142600-6144000	Enhancers	Esophagus	oesophagus
6	chr9:6142600-6144000	Enhancers	Pancreas	Pancrea
7	chr9:6142800-6143200	Enhancers	HepG2	liver

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