Variant report

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs12682158	0.82[CHB][hapmap]
rs1471558	0.82[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs1471560	0.85[CEU][hapmap];0.86[CHB][hapmap];0.92[GIH][hapmap];0.87[MEX][hapmap]
rs1481051	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1481058	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1481059	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1842538	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2955862	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2955923	0.83[EUR][1000 genomes]
rs2981139	0.80[EUR][1000 genomes]
rs2981191	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2981192	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2981194	0.83[EUR][1000 genomes]
rs2981195	0.82[EUR][1000 genomes]
rs7010922	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7824665	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv539555	chr8:39683857-40673606	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv534582	chr8:39884590-40653224	Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv1034355	chr8:39942179-39961432	Enhancers Weak transcription Flanking Active TSS Active 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
rs7828920	HGSNAT	cis	parietal	SCAN
rs7828920	STAR	cis	parietal	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:39950200-39955600	Weak transcription	Colon Smooth Muscle	Colon
2	chr8:39951000-39955400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr8:39951000-39955600	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr8:39951000-39958600	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr8:39951000-39968000	Weak transcription	Rectal Smooth Muscle	rectum
6	chr8:39951200-39955400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr8:39951200-39955600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr8:39952200-39955600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr8:39952600-39955600	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr8:39952600-39956400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr8:39952600-39957000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr8:39952600-39957000	Weak transcription	Placenta	Placenta
13	chr8:39954800-39958000	Enhancers	Rectal Mucosa Donor 31	rectum
14	chr8:39955000-39955400	Weak transcription	Stomach Mucosa	stomach
15	chr8:39955000-39957000	Enhancers	A549	lung
16	chr8:39955200-39955400	Enhancers	Sigmoid Colon	Sigmoid Colon
17	chr8:39955200-39956000	Enhancers	HUES64 Cell Line	embryonic stem cell
18	chr8:39955200-39956000	Enhancers	iPS-20b Cell Line	embryonic stem cell
19	chr8:39955200-39956400	Enhancers	Placenta Amnion	Placenta Amnion
20	chr8:39955200-39957000	Enhancers	Hela-S3	cervix
21	chr8:39955200-39957600	Enhancers	Rectal Mucosa Donor 29	rectum

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