Variant report

Variant	rs9858717
Chromosome Location	chr3:162015074-162015075
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1026691	1.00[CHB][hapmap]
rs1026693	1.00[CHB][hapmap]
rs11709562	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12492912	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13315794	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1488567	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2405562	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2405572	1.00[ASN][1000 genomes]
rs2897217	1.00[ASN][1000 genomes]
rs62290512	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62290513	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62290514	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7429198	1.00[ASN][1000 genomes]
rs7651879	1.00[ASN][1000 genomes]
rs936943	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs959804	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9820198	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9833330	1.00[ASN][1000 genomes]
rs9850476	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9851503	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9866575	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9880820	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv460919	chr3:161799090-162094430	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	nsv592144	chr3:161799090-162094430	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	esv2751981	chr3:161863459-162016298	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv877721	chr3:161878713-162303276	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv1006802	chr3:161921063-162599175	Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9858717	NAB1	trans	parietal	SCAN
rs9858717	ARHGEF6	trans	lymphoblastoid	seeQTL

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:162010800-162017200	Weak transcription	Rectal Smooth Muscle	rectum
2	chr3:162013200-162015800	Enhancers	Colon Smooth Muscle	Colon
3	chr3:162014000-162020800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr3:162014600-162016400	Weak transcription	HMEC	breast

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