Variant report

Variant	rs9457840
Chromosome Location	chr6:160541348-160541349
allele	C/T
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	FOXA1	chr6:160541138-160541440	HepG2	liver:	n/a	n/a
2	FOXA2	chr6:160541184-160541481	HepG2	liver:	n/a	n/a
3	HNF4A	chr6:160541181-160541447	HepG2	liver:	n/a	n/a
4	FOXA1	chr6:160541021-160541848	HepG2	liver:	n/a	n/a
5	FOXA1	chr6:160541086-160541789	HepG2	liver:	n/a	n/a
6	MXI1	chr6:160541277-160541364	HepG2	liver:	n/a	n/a
7	FOXA1	chr6:160541083-160541448	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:160528947..160531777-chr6:160539028..160541745,2	K562	blood:
2	chr6:160539183..160541787-chr6:160543102..160544828,2	K562	blood:

Variant related genes	Relation type
SLC22A1	TF binding region
ENSG00000270949	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10080371	0.82[ASN][1000 genomes]
rs11969663	1.00[TSI][hapmap]
rs1963529	0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2230044	0.93[GIH][hapmap];1.00[MEX][hapmap]
rs2282137	1.00[MEX][hapmap]
rs2282143	0.85[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2297360	0.93[GIH][hapmap]
rs2297361	0.93[GIH][hapmap];1.00[MEX][hapmap]
rs3777401	0.93[GIH][hapmap];1.00[MEX][hapmap]
rs3798170	0.89[ASN][1000 genomes]
rs3798175	1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6911252	1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6932293	0.87[ASN][1000 genomes]
rs73598455	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs8191959	0.91[JPT][hapmap];1.00[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9457833	0.93[GIH][hapmap];1.00[MEX][hapmap]
rs9457834	0.93[GIH][hapmap];1.00[MEX][hapmap]
rs9457839	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:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:160526200-160548600	Weak transcription	K562	blood
2	chr6:160526800-160545000	Weak transcription	HMEC	breast
3	chr6:160527000-160545000	Weak transcription	NHDF-Ad	bronchial
4	chr6:160527400-160549200	Weak transcription	Colonic Mucosa	Colon
5	chr6:160527400-160550000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr6:160529400-160548000	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr6:160529400-160559200	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr6:160530400-160548600	Weak transcription	Rectal Smooth Muscle	rectum
9	chr6:160530600-160543000	Weak transcription	Fetal Lung	lung
10	chr6:160530800-160542800	Weak transcription	Right Atrium	heart
11	chr6:160530800-160553400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr6:160531400-160545400	Weak transcription	NHLF	lung
13	chr6:160532200-160542400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr6:160533400-160552800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr6:160534400-160544200	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr6:160538800-160557600	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr6:160539000-160541600	Weak transcription	Stomach Smooth Muscle	stomach
18	chr6:160539000-160544200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr6:160539000-160546800	Weak transcription	NHEK	skin
20	chr6:160539000-160553000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr6:160539200-160543000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr6:160539200-160545800	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr6:160539400-160541400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr6:160539400-160542200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr6:160539400-160543400	Weak transcription	Fetal Muscle Leg	muscle
26	chr6:160539400-160544800	Weak transcription	Thymus	Thymus
27	chr6:160539400-160545400	Weak transcription	Duodenum Mucosa	Duodenum
28	chr6:160539400-160546200	Weak transcription	Brain Cingulate Gyrus	brain
29	chr6:160539400-160554200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr6:160539400-160554800	Weak transcription	Spleen	Spleen
31	chr6:160539400-160558000	Weak transcription	Gastric	stomach
32	chr6:160539400-160559400	Weak transcription	Brain Angular Gyrus	brain
33	chr6:160539400-160559400	Weak transcription	HSMMtube	muscle
34	chr6:160539400-160559600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr6:160539400-160580400	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr6:160539600-160553400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr6:160539600-160574600	Weak transcription	Adipose Nuclei	Adipose
38	chr6:160539800-160541800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr6:160539800-160542800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr6:160539800-160542800	Weak transcription	Pancreas	Pancrea
41	chr6:160539800-160544800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr6:160539800-160549000	Weak transcription	Primary T cells from cord blood	blood
43	chr6:160539800-160553400	Weak transcription	Ovary	ovary
44	chr6:160540000-160543000	Weak transcription	Lung	lung
45	chr6:160540000-160545600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr6:160540200-160542400	Enhancers	HepG2	liver
47	chr6:160540200-160542800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr6:160540200-160542800	Weak transcription	Fetal Muscle Trunk	muscle
49	chr6:160540200-160542800	Weak transcription	Fetal Stomach	stomach
50	chr6:160540200-160543000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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