Variant report

Variant	rs6458972
Chromosome Location	chr6:53755300-53755301
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:53656861..53659130-chr6:53753774..53755899,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228614	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10948779	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.87[YRI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13220665	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs2745461	0.83[EUR][1000 genomes]
rs2745462	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2820215	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2820216	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3000997	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3000999	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3001000	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3001001	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3001002	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3001009	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3003489	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3003491	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3003493	0.94[CEU][hapmap];0.88[EUR][1000 genomes]
rs3813849	0.87[CEU][hapmap];1.00[CHB][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.82[TSI][hapmap]
rs4236113	0.94[CEU][hapmap];0.91[YRI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4236115	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4265033	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4276502	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4286781	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4321822	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4336450	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4351263	0.94[CEU][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.82[TSI][hapmap];0.91[YRI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4382260	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4398733	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4437471	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4484515	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4489155	0.87[CEU][hapmap];1.00[CHB][hapmap];0.80[GIH][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.82[TSI][hapmap]
rs4591854	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4613824	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4615391	0.81[AMR][1000 genomes]
rs4712048	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4712049	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4715424	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs4715426	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6458957	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6458958	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6458959	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6458961	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6458962	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6458965	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6458966	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6458969	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6458971	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6650996	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6901644	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6920743	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6924025	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6926478	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6937901	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs742524	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs7739965	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7753504	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7754791	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7759946	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap]
rs7762883	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7763081	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7763147	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7769893	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7774173	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9296719	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9296721	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9367544	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.82[TSI][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9370235	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9370239	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.83[YRI][hapmap];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9382234	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs9382237	0.84[EUR][1000 genomes]
rs9382250	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9395886	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9474694	1.00[CHB][hapmap]

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	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	nsv830664	chr6:53698021-53825270	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53709800-53762200	Weak transcription	Primary B cells from cord blood	blood
2	chr6:53730200-53758800	Weak transcription	Brain Anterior Caudate	brain
3	chr6:53732000-53760400	Weak transcription	Aorta	Aorta
4	chr6:53735400-53755600	Weak transcription	HUVEC	blood vessel
5	chr6:53737800-53768400	Weak transcription	Esophagus	oesophagus
6	chr6:53739000-53767800	Weak transcription	Ovary	ovary
7	chr6:53739000-53771800	Weak transcription	Pancreas	Pancrea
8	chr6:53740400-53761000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr6:53741800-53760800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr6:53742200-53760800	Weak transcription	Fetal Intestine Large	intestine
11	chr6:53742200-53766200	Weak transcription	Fetal Stomach	stomach
12	chr6:53742400-53758800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr6:53743000-53761800	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr6:53744000-53762400	Weak transcription	Placenta	Placenta
15	chr6:53744600-53764200	Weak transcription	Fetal Intestine Small	intestine
16	chr6:53744800-53760400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr6:53745400-53760600	Weak transcription	Colon Smooth Muscle	Colon
18	chr6:53745600-53762200	Weak transcription	Duodenum Mucosa	Duodenum
19	chr6:53746200-53757200	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr6:53746200-53758000	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr6:53746400-53758600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr6:53746400-53762000	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr6:53746800-53762000	Weak transcription	Primary B cells from peripheral blood	blood
24	chr6:53746800-53768400	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr6:53747600-53767800	Weak transcription	Small Intestine	intestine
26	chr6:53749000-53761800	Weak transcription	Primary hematopoietic stem cells	blood
27	chr6:53749200-53763600	Weak transcription	Rectal Smooth Muscle	rectum
28	chr6:53749200-53765800	Weak transcription	Primary T cells from cord blood	blood
29	chr6:53749400-53762600	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr6:53750600-53760200	Weak transcription	HepG2	liver
31	chr6:53751600-53755400	Enhancers	iPS-18 Cell Line	embryonic stem cell
32	chr6:53752200-53756000	Enhancers	HUES48 Cell Line	embryonic stem cell
33	chr6:53752400-53757200	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr6:53752400-53758800	Weak transcription	Brain Angular Gyrus	brain
35	chr6:53752400-53761200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr6:53752400-53771000	Weak transcription	Gastric	stomach
37	chr6:53752400-53771800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr6:53752600-53756400	Weak transcription	Brain Substantia Nigra	brain
39	chr6:53752600-53758800	Weak transcription	Brain Cingulate Gyrus	brain
40	chr6:53752800-53755800	Weak transcription	Dnd41	blood
41	chr6:53752800-53757200	Weak transcription	Brain Hippocampus Middle	brain
42	chr6:53752800-53757400	Weak transcription	Thymus	Thymus
43	chr6:53752800-53782000	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr6:53753800-53756200	Enhancers	iPS-20b Cell Line	embryonic stem cell
45	chr6:53754000-53756000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr6:53754200-53758200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr6:53754200-53758800	Weak transcription	HMEC	breast
48	chr6:53754200-53758800	Weak transcription	NHEK	skin
49	chr6:53754400-53759000	Weak transcription	HSMM	muscle
50	chr6:53754400-53760800	Weak transcription	NH-A	brain

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