Variant report

Variant	rs2409811
Chromosome Location	chr8:11547971-11547972
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 9 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs12550668	0.80[ASW][hapmap]
rs2409809	0.96[CEU][hapmap];0.94[CHB][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2409810	0.91[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];0.84[CHD][hapmap];0.86[GIH][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2898293	0.91[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];0.84[CHD][hapmap];0.86[GIH][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[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	nsv529399	chr8:10970091-11805960	Enhancers Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	nsv1017865	chr8:11377795-11579954	Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1018978	chr8:11438267-11858466	Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv917963	chr8:11540723-11751798	Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv1027378	chr8:11541739-11858466	Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2409811	DEFB136	cis	parietal	SCAN
rs2409811	BLK	cis	lymphoblastoid	seeQTL
rs2409811	FLJ10661	cis	cerebellum	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:11541800-11549400	Enhancers	Fetal Heart	heart
2	chr8:11544800-11549200	Enhancers	Stomach Mucosa	stomach
3	chr8:11544800-11549400	Weak transcription	Ovary	ovary
4	chr8:11547000-11549400	Enhancers	Liver	Liver
5	chr8:11547000-11550000	Enhancers	Gastric	stomach
6	chr8:11547200-11550000	Enhancers	Pancreas	Pancrea
7	chr8:11547600-11549000	Enhancers	Duodenum Mucosa	Duodenum
8	chr8:11547800-11548800	Weak transcription	Left Ventricle	heart
9	chr8:11547800-11549200	Enhancers	Fetal Intestine Small	intestine
10	chr8:11547800-11549400	Weak transcription	Right Ventricle	heart
11	chr8:11547800-11549800	Weak transcription	Right Atrium	heart

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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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