Variant report

Variant	rs809204
Chromosome Location	chr8:11619163-11619164
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:11618295..11620623-chr8:11664020..11665628,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C8orf49-1	chr8:11618765-11620732	NONHSAT125071

Variant related genes	Relation type
ENSG00000079459	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs12677897	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17153755	0.84[CEU][hapmap];0.96[MEX][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17153785	0.88[CHB][hapmap];0.86[CHD][hapmap];0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs17810889	0.81[CHB][hapmap];0.80[CHD][hapmap]
rs2645450	0.80[CHD][hapmap];0.88[JPT][hapmap]
rs2645456	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2686208	0.98[EUR][1000 genomes]
rs2740444	0.81[CHD][hapmap];0.81[JPT][hapmap]
rs3203358	0.84[EUR][1000 genomes]
rs3729854	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3802168	1.00[YRI][hapmap]
rs6982453	0.83[JPT][hapmap]
rs804256	0.96[CEU][hapmap];0.84[CHD][hapmap];0.83[JPT][hapmap];0.88[MEX][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs804282	0.80[MEX][hapmap]
rs804287	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs804288	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs809203	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs809205	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8191544	0.85[CHB][hapmap];1.00[YRI][hapmap]
rs8191592	0.87[CHB][hapmap];1.00[YRI][hapmap]
rs8191594	0.81[JPT][hapmap]
rs904018	0.95[CEU][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	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
3	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
4	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
5	nsv1028229	chr8:11575762-11805961	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv539475	chr8:11575762-11805961	Flanking Active TSS Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	nsv428514	chr8:11580381-11765706	Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
8	nsv916483	chr8:11590294-11672038	Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
9	nsv1034014	chr8:11602337-11858466	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
10	nsv890360	chr8:11619163-11639991	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs809204	C8orf74	cis	parietal	SCAN
rs809204	NEIL2	cis	Nerve Tibial	GTEx
rs809204	GATA4	cis	multi-tissue	Pritchard
rs809204	C8orf49	cis	multi-tissue	Pritchard
rs809204	GATA4	cis	Liver	GTEx

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:11607000-11622800	Weak transcription	Stomach Mucosa	stomach
2	chr8:11608800-11619400	Strong transcription	Duodenum Mucosa	Duodenum
3	chr8:11610600-11621200	Strong transcription	Fetal Intestine Small	intestine
4	chr8:11614400-11619200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr8:11615800-11626800	Weak transcription	Left Ventricle	heart
6	chr8:11617000-11622800	Weak transcription	Fetal Heart	heart
7	chr8:11617000-11623000	Weak transcription	Placenta	Placenta
8	chr8:11617000-11626800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr8:11617200-11619400	Weak transcription	HSMMtube	muscle
10	chr8:11617200-11619600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr8:11617400-11619200	Weak transcription	Right Ventricle	heart
12	chr8:11617400-11619400	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr8:11617400-11619400	Weak transcription	HSMM	muscle
14	chr8:11617400-11620000	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr8:11617400-11622800	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr8:11617400-11623200	Weak transcription	HepG2	liver
17	chr8:11617400-11626000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr8:11617400-11626400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr8:11617400-11626800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr8:11617800-11619200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr8:11618000-11626000	Weak transcription	Pancreas	Pancrea
22	chr8:11618000-11626800	Weak transcription	Fetal Intestine Large	intestine
23	chr8:11618200-11619200	Weak transcription	Gastric	stomach
24	chr8:11618200-11619400	Enhancers	NH-A	brain
25	chr8:11618400-11623000	Weak transcription	Liver	Liver
26	chr8:11618600-11619400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr8:11618600-11619800	Weak transcription	Ovary	ovary
28	chr8:11618800-11619400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr8:11618800-11620800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr8:11619000-11619200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr8:11619000-11619600	Enhancers	K562	blood
32	chr8:11619000-11620200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr8:11619000-11621800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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