Variant report

Variant	rs9457839
Chromosome Location	chr6:160538020-160538021
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:160537967-160538065	K562	blood:	n/a	n/a
2	POLR2A	chr6:160537830-160538020	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:160534504..160540683-chr6:160541496..160546529,8	K562	blood:

Variant related genes	Relation type
SLC22A1	TF binding region
ENSG00000175003	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10080371	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1116262	0.84[CHB][hapmap];0.83[EUR][1000 genomes]
rs1963529	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2230044	0.84[CHB][hapmap];0.93[GIH][hapmap];1.00[EUR][1000 genomes]
rs2282137	0.84[CHB][hapmap];1.00[EUR][1000 genomes]
rs2282143	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2297359	0.84[CHB][hapmap];1.00[EUR][1000 genomes]
rs2297360	0.84[CHB][hapmap];0.93[GIH][hapmap];1.00[EUR][1000 genomes]
rs2297361	0.84[CHB][hapmap];0.93[GIH][hapmap];1.00[EUR][1000 genomes]
rs2777355	1.00[EUR][1000 genomes]
rs3777401	0.84[CHB][hapmap];0.93[GIH][hapmap];1.00[EUR][1000 genomes]
rs3777402	0.84[CHB][hapmap];1.00[EUR][1000 genomes]
rs3777406	0.84[CHB][hapmap]
rs3798170	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3798175	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6911252	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6925867	1.00[EUR][1000 genomes]
rs6932293	0.97[ASN][1000 genomes]
rs73598455	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8191855	1.00[EUR][1000 genomes]
rs8191893	0.84[CHB][hapmap];1.00[EUR][1000 genomes]
rs8191912	0.81[CHB][hapmap];1.00[EUR][1000 genomes]
rs8191921	1.00[EUR][1000 genomes]
rs8191959	0.92[CHB][hapmap];0.90[JPT][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9456502	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9457816	1.00[EUR][1000 genomes]
rs9457829	1.00[EUR][1000 genomes]
rs9457833	0.84[CHB][hapmap];0.93[GIH][hapmap];1.00[EUR][1000 genomes]
rs9457834	0.84[CHB][hapmap];0.93[GIH][hapmap];1.00[EUR][1000 genomes]
rs9457840	0.84[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.94[MKK][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[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	esv2758089	chr6:160372244-161234665	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	esv2759484	chr6:160372244-161234665	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	esv35098	chr6:160422589-161070870	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	esv2757197	chr6:160432331-161070870	Weak transcription Genic enhancers Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv818463	chr6:160435569-161025547	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:160512000-160539200	Weak transcription	Stomach Mucosa	stomach
2	chr6:160523200-160540200	Weak transcription	Fetal Heart	heart
3	chr6:160526200-160539000	Weak transcription	Colon Smooth Muscle	Colon
4	chr6:160526200-160548600	Weak transcription	K562	blood
5	chr6:160526800-160538600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr6:160526800-160540600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr6:160526800-160545000	Weak transcription	HMEC	breast
8	chr6:160527000-160538800	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr6:160527000-160545000	Weak transcription	NHDF-Ad	bronchial
10	chr6:160527200-160541200	Weak transcription	Osteobl	bone
11	chr6:160527400-160538400	Weak transcription	Brain Cingulate Gyrus	brain
12	chr6:160527400-160538800	Weak transcription	Brain Hippocampus Middle	brain
13	chr6:160527400-160549200	Weak transcription	Colonic Mucosa	Colon
14	chr6:160527400-160550000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr6:160527600-160541200	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr6:160528000-160538400	Weak transcription	Ovary	ovary
17	chr6:160529000-160539600	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr6:160529200-160538200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr6:160529200-160538400	Weak transcription	Brain Anterior Caudate	brain
20	chr6:160529200-160538400	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr6:160529200-160538800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr6:160529400-160538200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr6:160529400-160538200	Weak transcription	Brain Substantia Nigra	brain
24	chr6:160529400-160538400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr6:160529400-160538400	Weak transcription	Esophagus	oesophagus
26	chr6:160529400-160548000	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr6:160529400-160559200	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr6:160529600-160538200	Weak transcription	Pancreas	Pancrea
29	chr6:160529600-160538600	Weak transcription	Brain Angular Gyrus	brain
30	chr6:160530400-160548600	Weak transcription	Rectal Smooth Muscle	rectum
31	chr6:160530600-160543000	Weak transcription	Fetal Lung	lung
32	chr6:160530800-160542800	Weak transcription	Right Atrium	heart
33	chr6:160530800-160553400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr6:160531000-160538400	Weak transcription	Stomach Smooth Muscle	stomach
35	chr6:160531000-160538800	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr6:160531400-160538600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr6:160531400-160545400	Weak transcription	NHLF	lung
38	chr6:160531600-160538400	Weak transcription	Duodenum Mucosa	Duodenum
39	chr6:160531600-160538600	Weak transcription	NHEK	skin
40	chr6:160532000-160538200	Weak transcription	Primary neutrophils fromperipheralblood	blood
41	chr6:160532000-160538400	Weak transcription	Primary B cells from cord blood	blood
42	chr6:160532000-160538800	Weak transcription	Adipose Nuclei	Adipose
43	chr6:160532200-160542400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr6:160532800-160538200	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr6:160533400-160538200	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr6:160533400-160538200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr6:160533400-160552800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr6:160534000-160539800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr6:160534400-160538200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr6:160534400-160538200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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