Variant report

Variant	rs10948779
Chromosome Location	chr6:53663604-53663605
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	chr6:53663341..53666059-chr6:53671400..53673766,2	MCF-7	breast:

Extended variants
information (count: 90 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11755346	0.89[EUR][1000 genomes]
rs13220665	0.94[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes]
rs2745462	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2820215	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2820216	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3000996	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3000997	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]
rs3000999	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3001000	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3001001	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3001002	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3001009	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3001010	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3003489	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3003491	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3003493	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3003500	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3003501	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34165049	0.83[EUR][1000 genomes]
rs34861916	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34880762	0.89[EUR][1000 genomes]
rs35389351	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35517171	0.89[EUR][1000 genomes]
rs35756855	0.87[EUR][1000 genomes]
rs3813849	0.94[CEU][hapmap];1.00[CHB][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4236113	1.00[CEU][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4236115	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4265033	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4276502	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4286781	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4321822	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4326237	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4336450	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4351263	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4382260	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4398733	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4437471	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4484515	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4489155	0.94[CEU][hapmap];1.00[CHB][hapmap];0.80[GIH][hapmap];1.00[MEX][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4591854	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4615391	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4712048	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4712049	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4715424	0.94[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4715426	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59641455	0.89[EUR][1000 genomes]
rs60035355	0.89[EUR][1000 genomes]
rs6458957	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6458958	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6458959	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6458961	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6458962	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6458965	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6458966	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6458969	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6458971	0.87[EUR][1000 genomes]
rs6458972	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]
rs6650996	0.89[AFR][1000 genomes];1.00[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];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6924025	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6925836	0.89[EUR][1000 genomes]
rs6926478	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6937901	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs71555560	0.89[EUR][1000 genomes]
rs742524	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7739965	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7753504	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7754791	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7759946	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[MEX][hapmap];0.89[EUR][1000 genomes]
rs7762883	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7763081	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7763147	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7769893	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7774173	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9296719	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9296721	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9367544	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9370235	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9370239	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9382234	0.94[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9382237	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9382250	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9395886	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10948779	POTEG	trans	lymphoblastoid	seeQTL

Chromatin state (count:56 , 50 per page) page: 1 2

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	chr6:53661600-53664000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr6:53661600-53665000	Weak transcription	Primary hematopoietic stem cells	blood
12	chr6:53661600-53665800	Weak transcription	NHLF	lung
13	chr6:53661800-53664000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr6:53662000-53670200	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr6:53662200-53665800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr6:53662200-53667200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr6:53662400-53664000	Weak transcription	Colon Smooth Muscle	Colon
18	chr6:53662400-53664200	Enhancers	Rectal Mucosa Donor 31	rectum
19	chr6:53662400-53664600	Weak transcription	Brain Substantia Nigra	brain
20	chr6:53662400-53667400	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr6:53662400-53668000	Weak transcription	NH-A	brain
22	chr6:53662600-53663800	Weak transcription	Placenta	Placenta
23	chr6:53662600-53664000	Weak transcription	Brain Cingulate Gyrus	brain
24	chr6:53662600-53664200	Weak transcription	Hela-S3	cervix
25	chr6:53662600-53664800	Enhancers	HepG2	liver
26	chr6:53662600-53665800	Weak transcription	Brain Anterior Caudate	brain
27	chr6:53662600-53666800	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr6:53662600-53666800	Weak transcription	Stomach Smooth Muscle	stomach
29	chr6:53662600-53668000	Weak transcription	Pancreas	Pancrea
30	chr6:53662600-53669600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr6:53662600-53670000	Weak transcription	Esophagus	oesophagus
32	chr6:53662600-53670400	Weak transcription	Thymus	Thymus
33	chr6:53662600-53677600	Weak transcription	Small Intestine	intestine
34	chr6:53662800-53667800	Weak transcription	Rectal Smooth Muscle	rectum
35	chr6:53662800-53668000	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr6:53662800-53668000	Weak transcription	NHEK	skin
37	chr6:53662800-53669800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr6:53662800-53669800	Weak transcription	HMEC	breast
39	chr6:53662800-53670200	Weak transcription	Fetal Intestine Large	intestine
40	chr6:53662800-53670200	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr6:53662800-53675400	Weak transcription	Duodenum Mucosa	Duodenum
42	chr6:53663000-53664000	Weak transcription	Brain Hippocampus Middle	brain
43	chr6:53663000-53664400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr6:53663000-53669800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr6:53663200-53670600	Weak transcription	Fetal Intestine Small	intestine
46	chr6:53663400-53664800	Enhancers	Fetal Thymus	thymus
47	chr6:53663600-53663800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr6:53663600-53663800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr6:53663600-53663800	Flanking Active TSS	Dnd41	blood
50	chr6:53663600-53664000	Enhancers	ES-WA7 Cell Line	embryonic stem cell

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