Variant report

Variant	rs3000997
Chromosome Location	chr6:53666266-53666267
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:53664733..53666465-chr6:53680416..53681978,2	MCF-7	breast:
2	chr6:53658074..53661500-chr6:53665501..53670163,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137269	Chromatin interaction
ENSG00000228614	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10948779	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11755346	0.89[EUR][1000 genomes]
rs13220665	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2745462	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2820215	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2820216	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[YRI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3000996	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3000999	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3001000	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3001001	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3001002	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3001009	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3001010	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3003489	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3003491	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3003493	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3003500	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3003501	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34165049	0.83[EUR][1000 genomes]
rs34861916	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34880762	0.89[EUR][1000 genomes]
rs35389351	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35517171	0.89[EUR][1000 genomes]
rs35756855	0.80[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs3813849	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4236113	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4236115	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4265033	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4276502	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4286781	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4321822	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4326237	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4336450	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4351263	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4382260	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4398733	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4437471	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4484515	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4489155	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4591854	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4615391	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4712048	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4712049	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4715424	0.94[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4715426	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59641455	0.89[EUR][1000 genomes]
rs60035355	0.89[EUR][1000 genomes]
rs6458957	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6458958	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6458959	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6458961	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6458962	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6458965	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6458966	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6458969	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6458971	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6458972	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]
rs6650996	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6899752	0.89[EUR][1000 genomes]
rs6901644	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6920743	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6924025	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6925836	0.89[EUR][1000 genomes]
rs6926478	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6937901	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71555560	0.89[EUR][1000 genomes]
rs742524	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7739965	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7753504	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7754791	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7759946	0.94[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes]
rs7762883	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7763081	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7763147	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7769893	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7774173	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9296719	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9296721	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9367544	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9370235	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9370239	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9382234	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9382237	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9382250	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9395886	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9474694	1.00[CHB][hapmap]

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:50 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53661400-53666400	Weak transcription	Primary B cells from cord blood	blood
2	chr6:53661400-53666600	Weak transcription	Aorta	Aorta
3	chr6:53661400-53667200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr6:53661400-53668000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr6:53661400-53668000	Weak transcription	Ovary	ovary
6	chr6:53661400-53669800	Weak transcription	Gastric	stomach
7	chr6:53661400-53670400	Weak transcription	Primary T cells from cord blood	blood
8	chr6:53661400-53675600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr6:53661400-53688200	Weak transcription	Right Ventricle	heart
10	chr6:53662000-53670200	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr6:53662200-53667200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr6:53662400-53667400	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr6:53662400-53668000	Weak transcription	NH-A	brain
14	chr6:53662600-53666800	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr6:53662600-53666800	Weak transcription	Stomach Smooth Muscle	stomach
16	chr6:53662600-53668000	Weak transcription	Pancreas	Pancrea
17	chr6:53662600-53669600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr6:53662600-53670000	Weak transcription	Esophagus	oesophagus
19	chr6:53662600-53670400	Weak transcription	Thymus	Thymus
20	chr6:53662600-53677600	Weak transcription	Small Intestine	intestine
21	chr6:53662800-53667800	Weak transcription	Rectal Smooth Muscle	rectum
22	chr6:53662800-53668000	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr6:53662800-53668000	Weak transcription	NHEK	skin
24	chr6:53662800-53669800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr6:53662800-53669800	Weak transcription	HMEC	breast
26	chr6:53662800-53670200	Weak transcription	Fetal Intestine Large	intestine
27	chr6:53662800-53670200	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr6:53662800-53675400	Weak transcription	Duodenum Mucosa	Duodenum
29	chr6:53663000-53669800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr6:53663200-53670600	Weak transcription	Fetal Intestine Small	intestine
31	chr6:53664000-53668000	Weak transcription	HUVEC	blood vessel
32	chr6:53664000-53669000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr6:53664800-53667200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr6:53664800-53668400	Weak transcription	HepG2	liver
35	chr6:53664800-53669800	Weak transcription	Fetal Thymus	thymus
36	chr6:53664800-53673400	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr6:53665000-53667800	Weak transcription	Brain Substantia Nigra	brain
38	chr6:53665000-53669800	Weak transcription	Brain Cingulate Gyrus	brain
39	chr6:53665000-53674800	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr6:53665000-53675600	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr6:53665800-53666400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr6:53665800-53666400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr6:53665800-53666400	Enhancers	NHLF	lung
44	chr6:53665800-53667600	Enhancers	Brain Hippocampus Middle	brain
45	chr6:53665800-53667800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr6:53665800-53668800	Enhancers	Dnd41	blood
47	chr6:53666000-53666400	Enhancers	Colon Smooth Muscle	Colon
48	chr6:53666000-53670000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr6:53666200-53668200	Weak transcription	Brain Anterior Caudate	brain
50	chr6:53666200-53669800	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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