Variant report

Variant	rs7739965
Chromosome Location	chr6:53679798-53679799
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:53678291..53681070-chr6:53681168..53683223,2	MCF-7	breast:

Extended variants
information (count: 87 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10948779	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11755346	0.85[EUR][1000 genomes]
rs13220665	0.87[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs2745462	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2820215	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2820216	0.94[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3000996	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3000997	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3000999	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3001000	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3001001	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3001002	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3001009	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3001010	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3003489	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3003491	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3003493	0.94[CEU][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3003500	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3003501	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34861916	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34880762	0.85[EUR][1000 genomes]
rs35389351	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35517171	0.85[EUR][1000 genomes]
rs35756855	0.82[EUR][1000 genomes]
rs3813849	0.87[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4236113	0.94[CEU][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4236115	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4265033	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4276502	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4286781	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4321822	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4326237	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4336450	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4351263	0.94[CEU][hapmap];0.95[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4382260	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4398733	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4437471	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4484515	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4489155	0.87[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4591854	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4615391	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4712048	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4712049	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4715424	0.87[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4715426	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs59641455	0.85[EUR][1000 genomes]
rs60035355	0.85[EUR][1000 genomes]
rs6458957	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6458958	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6458959	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6458961	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6458962	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6458965	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6458966	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6458969	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6458971	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6458972	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6650996	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6899752	0.85[EUR][1000 genomes]
rs6901644	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6920743	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6924025	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6925836	0.85[EUR][1000 genomes]
rs6926478	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6937901	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs71555560	0.85[EUR][1000 genomes]
rs742524	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7753504	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7754791	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7759946	0.87[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs7762883	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7763081	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7763147	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7769893	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7774173	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9296719	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9296721	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9367544	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9370235	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9370239	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9382234	0.87[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9382237	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9382250	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9395886	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9474694	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 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

No data

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53661400-53688200	Weak transcription	Right Ventricle	heart
2	chr6:53668200-53680200	Weak transcription	Fetal Stomach	stomach
3	chr6:53668800-53680000	Weak transcription	Rectal Smooth Muscle	rectum
4	chr6:53668800-53683800	Weak transcription	Ovary	ovary
5	chr6:53670200-53686400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr6:53670800-53680000	Weak transcription	Stomach Smooth Muscle	stomach
7	chr6:53670800-53693200	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr6:53671000-53680200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr6:53671000-53683600	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr6:53671200-53680400	Weak transcription	Fetal Brain Female	brain
11	chr6:53673400-53687200	Weak transcription	Fetal Muscle Leg	muscle
12	chr6:53673600-53682800	Weak transcription	Dnd41	blood
13	chr6:53674800-53680400	Enhancers	Fetal Intestine Small	intestine
14	chr6:53675000-53681200	Weak transcription	Fetal Brain Male	brain
15	chr6:53675400-53680200	Enhancers	Stomach Mucosa	stomach
16	chr6:53675400-53680400	Enhancers	Sigmoid Colon	Sigmoid Colon
17	chr6:53676200-53683600	Weak transcription	Left Ventricle	heart
18	chr6:53676200-53697800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr6:53676400-53679800	Weak transcription	Fetal Heart	heart
20	chr6:53676800-53679800	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr6:53676800-53680000	Weak transcription	Pancreas	Pancrea
22	chr6:53676800-53680400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr6:53676800-53680400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr6:53676800-53686800	Weak transcription	Right Atrium	heart
25	chr6:53676800-53687200	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr6:53677000-53680000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr6:53677400-53680600	Enhancers	Fetal Intestine Large	intestine
28	chr6:53677600-53680400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr6:53677600-53680600	Enhancers	Brain Anterior Caudate	brain
30	chr6:53677600-53680600	Enhancers	Small Intestine	intestine
31	chr6:53677600-53680600	Enhancers	HepG2	liver
32	chr6:53677800-53681600	Enhancers	Brain Hippocampus Middle	brain
33	chr6:53678000-53679800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr6:53678000-53680000	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr6:53678000-53683600	Weak transcription	HMEC	breast
36	chr6:53678200-53680000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr6:53678200-53680200	Weak transcription	NHEK	skin
38	chr6:53678400-53679800	Weak transcription	HUVEC	blood vessel
39	chr6:53678400-53680200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr6:53678400-53680600	Enhancers	HUES48 Cell Line	embryonic stem cell
41	chr6:53678400-53681200	Enhancers	Brain Substantia Nigra	brain
42	chr6:53678400-53683600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr6:53678600-53679800	Enhancers	iPS-18 Cell Line	embryonic stem cell
44	chr6:53678600-53680200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr6:53678600-53680200	Weak transcription	Lung	lung
46	chr6:53678600-53680600	Enhancers	iPS-15b Cell Line	embryonic stem cell
47	chr6:53678600-53680600	Enhancers	iPS-20b Cell Line	embryonic stem cell
48	chr6:53678600-53681400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr6:53678600-53692200	Weak transcription	Esophagus	oesophagus
50	chr6:53678800-53679800	Weak transcription	H1 Cell Line	embryonic stem cell

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