Variant report

Variant	rs9873474
Chromosome Location	chr3:157173555-157173556
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11709669	0.82[CHB][hapmap]
rs11717115	0.87[ASW][hapmap]
rs12631456	0.94[CEU][hapmap];0.91[GIH][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1378794	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1378800	0.82[CHB][hapmap]
rs1456101	0.82[CHB][hapmap];0.80[CHD][hapmap]
rs1456102	0.87[CHB][hapmap]
rs17470517	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1824056	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1902347	0.99[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28690487	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4679795	0.82[CHB][hapmap]
rs4679798	0.94[CEU][hapmap];0.89[GIH][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4680370	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap]
rs57095742	0.94[EUR][1000 genomes]
rs7639175	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9815250	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9841781	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9851066	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9859018	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9877620	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757900	chr3:157090166-157254684	Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	esv2759193	chr3:157090166-157254684	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9873474	KPNA4	cis	parietal	SCAN
rs9873474	C3orf55	cis	cerebellum	SCAN
rs9873474	B3GALNT1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:157159000-157177400	Weak transcription	NH-A	brain
2	chr3:157160400-157195000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr3:157160600-157176800	Weak transcription	Pancreas	Pancrea
4	chr3:157161200-157186600	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr3:157162400-157177000	Weak transcription	HSMM	muscle
6	chr3:157163800-157177000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr3:157164600-157185400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr3:157164800-157176800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr3:157165200-157177200	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr3:157165800-157174400	Weak transcription	Osteobl	bone
11	chr3:157170200-157187000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr3:157171200-157175200	Weak transcription	HUVEC	blood vessel
13	chr3:157172000-157175000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr3:157172200-157176800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr3:157172200-157176800	Weak transcription	NHDF-Ad	bronchial
16	chr3:157172400-157177400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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