Variant report

Variant	rs6458957
Chromosome Location	chr6:53662056-53662057
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	chr6:53661875-53662255	HepG2	liver:	n/a	chr6:53662044-53662059
2	FOS	chr6:53661525-53662060	MCF10A-Er-Src	breast:	n/a	n/a
3	STAT3	chr6:53661601-53662106	MCF10A-Er-Src	breast:	n/a	chr6:53661806-53661815 chr6:53661693-53661701 chr6:53661805-53661814
4	STAT3	chr6:53661626-53662097	MCF10A-Er-Src	breast:	n/a	chr6:53661806-53661815 chr6:53661693-53661701 chr6:53661805-53661814
5	FOS	chr6:53661432-53662079	MCF10A-Er-Src	breast:	n/a	n/a
6	STAT3	chr6:53661618-53662125	MCF10A-Er-Src	breast:	n/a	chr6:53661806-53661815 chr6:53661693-53661701 chr6:53661805-53661814

No.	Distal block	Cell Line	Cell type
1	chr6:53656949..53662173-chr6:53781368..53784554,5	MCF-7	breast:
2	chr6:53610265..53615014-chr6:53656858..53662694,9	MCF-7	breast:
3	chr6:53652474..53654178-chr6:53661361..53663423,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228614	TF binding region
ENSG00000227885	Chromatin interaction
ENSG00000137269	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10948779	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11755346	0.89[EUR][1000 genomes]
rs13220665	0.89[EUR][1000 genomes]
rs2745462	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2820215	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2820216	0.87[EUR][1000 genomes]
rs3000996	0.94[EUR][1000 genomes]
rs3000997	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3000999	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3001000	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3001001	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3001002	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3001009	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3001010	0.94[EUR][1000 genomes]
rs3003489	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3003491	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3003493	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3003500	0.94[EUR][1000 genomes]
rs3003501	0.94[EUR][1000 genomes]
rs34165049	0.83[EUR][1000 genomes]
rs34861916	0.89[EUR][1000 genomes]
rs34880762	0.89[EUR][1000 genomes]
rs35389351	0.90[EUR][1000 genomes]
rs35517171	0.89[EUR][1000 genomes]
rs35756855	0.87[EUR][1000 genomes]
rs3813849	0.94[EUR][1000 genomes]
rs4236113	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4236115	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4265033	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4276502	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4286781	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4321822	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4326237	0.94[EUR][1000 genomes]
rs4336450	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4351263	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4382260	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4398733	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4437471	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4484515	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4489155	0.94[EUR][1000 genomes]
rs4591854	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4615391	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4712048	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4712049	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4715424	0.94[EUR][1000 genomes]
rs4715426	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59641455	0.89[EUR][1000 genomes]
rs60035355	0.89[EUR][1000 genomes]
rs6458958	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6458959	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6458961	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6458962	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6458965	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6458966	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6458969	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6458971	0.87[EUR][1000 genomes]
rs6458972	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6650996	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6899752	0.89[EUR][1000 genomes]
rs6901644	0.86[EUR][1000 genomes]
rs6920743	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6924025	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6925836	0.89[EUR][1000 genomes]
rs6926478	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6937901	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs71555560	0.89[EUR][1000 genomes]
rs7739965	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7753504	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7754791	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7759946	0.89[EUR][1000 genomes]
rs7762883	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7763081	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7763147	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7769893	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7774173	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9296719	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9296721	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9367544	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9370235	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9370239	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9382234	0.94[EUR][1000 genomes]
rs9382237	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9382250	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9395886	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034955	chr6:53447607-53931055	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1021506	chr6:53600338-53770482	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	esv3474747	chr6:53648744-53677210	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	esv3474748	chr6:53648758-53677207	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53657800-53662400	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr6:53660400-53663000	Flanking Active TSS	Dnd41	blood
3	chr6:53660800-53662800	Active TSS	Rectal Smooth Muscle	rectum
4	chr6:53660800-53663000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr6:53661000-53662200	Flanking Active TSS	HMEC	breast
6	chr6:53661200-53662200	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr6:53661200-53662400	Flanking Active TSS	NHEK	skin
8	chr6:53661200-53662600	Active TSS	Fetal Brain Female	brain
9	chr6:53661400-53662200	Weak transcription	Esophagus	oesophagus
10	chr6:53661400-53662200	Weak transcription	Pancreas	Pancrea
11	chr6:53661400-53662600	Flanking Active TSS	HepG2	liver
12	chr6:53661400-53662800	Active TSS	Rectal Mucosa Donor 29	rectum
13	chr6:53661400-53663600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr6:53661400-53666400	Weak transcription	Primary B cells from cord blood	blood
15	chr6:53661400-53666600	Weak transcription	Aorta	Aorta
16	chr6:53661400-53667200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr6:53661400-53668000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr6:53661400-53668000	Weak transcription	Ovary	ovary
19	chr6:53661400-53669800	Weak transcription	Gastric	stomach
20	chr6:53661400-53670400	Weak transcription	Primary T cells from cord blood	blood
21	chr6:53661400-53675600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr6:53661400-53688200	Weak transcription	Right Ventricle	heart
23	chr6:53661600-53662200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr6:53661600-53662200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr6:53661600-53662200	Enhancers	Muscle Satellite Cultured Cells	--
26	chr6:53661600-53662200	Flanking Active TSS	Brain Cingulate Gyrus	brain
27	chr6:53661600-53662200	Enhancers	Rectal Mucosa Donor 31	rectum
28	chr6:53661600-53662400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr6:53661600-53662400	Enhancers	NH-A	brain
30	chr6:53661600-53662600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr6:53661600-53662600	Enhancers	Cortex derived primary cultured neurospheres	brain
32	chr6:53661600-53662600	Enhancers	Brain Angular Gyrus	brain
33	chr6:53661600-53662600	Enhancers	Brain Anterior Caudate	brain
34	chr6:53661600-53662600	Flanking Active TSS	Fetal Intestine Small	intestine
35	chr6:53661600-53662600	Enhancers	Stomach Mucosa	stomach
36	chr6:53661600-53662800	Enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr6:53661600-53662800	Enhancers	Fetal Kidney	kidney
38	chr6:53661600-53663600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr6:53661600-53663600	Weak transcription	Colonic Mucosa	Colon
40	chr6:53661600-53664000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr6:53661600-53665000	Weak transcription	Primary hematopoietic stem cells	blood
42	chr6:53661600-53665800	Weak transcription	NHLF	lung
43	chr6:53661800-53662200	Active TSS	Brain Germinal Matrix	brain
44	chr6:53661800-53662200	Flanking Active TSS	Brain Hippocampus Middle	brain
45	chr6:53661800-53662200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
46	chr6:53661800-53662200	Active TSS	Duodenum Mucosa	Duodenum
47	chr6:53661800-53662400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr6:53661800-53662400	Enhancers	Brain Substantia Nigra	brain
49	chr6:53661800-53662400	Enhancers	Colon Smooth Muscle	Colon
50	chr6:53661800-53662600	Enhancers	Stomach Smooth Muscle	stomach

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