Variant report

Variant	rs9368501
Chromosome Location	chr6:27295082-27295083
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10946904	0.83[CHB][hapmap]
rs2092114	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2295603	0.85[CEU][hapmap];0.83[CHD][hapmap];0.98[GIH][hapmap]
rs2893911	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs3800319	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs4546474	0.86[ASW][hapmap];0.85[CEU][hapmap];0.83[CHB][hapmap];0.83[CHD][hapmap];0.90[GIH][hapmap]
rs4559087	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6909479	0.81[AMR][1000 genomes]
rs6910659	0.81[AMR][1000 genomes]
rs7744605	0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7746841	0.96[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7771953	0.90[EUR][1000 genomes]
rs9366689	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs9379968	0.86[ASW][hapmap];0.92[CEU][hapmap];0.89[CHB][hapmap];0.83[CHD][hapmap];0.90[GIH][hapmap];0.84[TSI][hapmap];0.80[AMR][1000 genomes]
rs9379973	0.84[EUR][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	nsv948921	chr6:26556890-27443957	Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	472 gene(s)	inside rSNPs	diseases
2	nsv1017328	chr6:27177147-27369588	Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	nsv883505	chr6:27210614-27300580	Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv883507	chr6:27279982-27318836	Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	esv1823942	chr6:27282284-27295506	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs9368501	ZNF323	cis	parietal	SCAN
rs9368501	AL022393.7	cis	Muscle Skeletal	GTEx
rs9368501	HIST1H2AL	cis	cerebellum	SCAN
rs9368501	ZSCAN23	cis	cerebellum	SCAN
rs9368501	BTN3A3	cis	cerebellum	SCAN
rs9368501	HIST1H4B	cis	parietal	SCAN
rs9368501	BTN3A3	cis	parietal	SCAN
rs9368501	ZSCAN23	cis	parietal	SCAN
rs9368501	BTN3A2	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27294800-27295200	Enhancers	HepG2	liver

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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