Variant report

Variant	rs6937901
Chromosome Location	chr6:53722488-53722489
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	chr6:53719967..53722619-chr6:53723859..53726928,3	MCF-7	breast:

Extended variants
information (count: 88 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10948779	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11755346	0.85[EUR][1000 genomes]
rs13220665	0.94[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs2745462	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2820215	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2820216	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3000996	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3000997	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3000999	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]
rs3001000	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3001001	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3001002	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3001009	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3001010	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3003489	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3003491	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3003493	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[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	0.83[EUR][1000 genomes]
rs3813849	0.94[CEU][hapmap];1.00[CHB][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4236113	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4236115	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4265033	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4276502	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4286781	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4321822	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4326237	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4336450	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4351263	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4382260	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4398733	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4437471	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4484515	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4489155	0.94[CEU][hapmap];1.00[CHB][hapmap];0.80[GIH][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4591854	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4615391	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4712048	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4712049	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4715424	0.94[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4715426	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59641455	0.85[EUR][1000 genomes]
rs60035355	0.85[EUR][1000 genomes]
rs6458957	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6458958	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6458959	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6458961	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6458962	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6458965	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6458966	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6458969	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6458971	0.91[EUR][1000 genomes];0.92[ASN][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];0.98[MKK][hapmap];0.82[TSI][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6650996	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6899752	0.85[EUR][1000 genomes]
rs6901644	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6920743	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6924025	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6925836	0.85[EUR][1000 genomes]
rs6926478	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71555560	0.85[EUR][1000 genomes]
rs742524	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7739965	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7753504	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7754791	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7759946	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs7762883	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7763081	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7763147	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7769893	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7774173	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9296719	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9296721	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9370235	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9370239	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9382234	0.94[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9382237	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9382250	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9395886	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6937901	POTEG	trans	lymphoblastoid	seeQTL

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53695000-53743200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:53703200-53726400	Weak transcription	Fetal Stomach	stomach
3	chr6:53703800-53727600	Weak transcription	Stomach Smooth Muscle	stomach
4	chr6:53709800-53762200	Weak transcription	Primary B cells from cord blood	blood
5	chr6:53717800-53731800	Weak transcription	Primary hematopoietic stem cells	blood
6	chr6:53718400-53723400	Enhancers	Stomach Mucosa	stomach
7	chr6:53718800-53723400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr6:53719800-53727600	Enhancers	Brain Substantia Nigra	brain
9	chr6:53719800-53727800	Enhancers	Brain Hippocampus Middle	brain
10	chr6:53719800-53747800	Weak transcription	Primary T cells from cord blood	blood
11	chr6:53720000-53722600	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr6:53720000-53723000	Enhancers	Left Ventricle	heart
13	chr6:53720000-53724000	Enhancers	Brain Cingulate Gyrus	brain
14	chr6:53720000-53724400	Enhancers	Brain Anterior Caudate	brain
15	chr6:53720000-53727600	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr6:53720200-53722600	Weak transcription	Colon Smooth Muscle	Colon
17	chr6:53720200-53723000	Enhancers	Right Atrium	heart
18	chr6:53720200-53723000	Enhancers	Right Ventricle	heart
19	chr6:53720400-53722800	Enhancers	HepG2	liver
20	chr6:53720400-53723000	Enhancers	Gastric	stomach
21	chr6:53720600-53741400	Weak transcription	Dnd41	blood
22	chr6:53720800-53736600	Weak transcription	Fetal Thymus	thymus
23	chr6:53721000-53723400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr6:53721200-53726200	Weak transcription	Fetal Intestine Small	intestine
25	chr6:53721200-53726400	Weak transcription	Fetal Intestine Large	intestine
26	chr6:53721200-53726600	Weak transcription	Rectal Smooth Muscle	rectum
27	chr6:53721200-53726800	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr6:53721400-53723000	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr6:53721400-53724200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr6:53721600-53723200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr6:53721600-53723200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr6:53721600-53723400	Enhancers	Esophagus	oesophagus
33	chr6:53721600-53728000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr6:53721800-53723400	Enhancers	HMEC	breast
35	chr6:53721800-53725600	Weak transcription	Aorta	Aorta
36	chr6:53721800-53726800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr6:53722000-53722600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr6:53722000-53722600	Enhancers	H9 Cell Line	embryonic stem cell
39	chr6:53722000-53722600	Enhancers	iPS-15b Cell Line	embryonic stem cell
40	chr6:53722000-53722600	Enhancers	iPS-18 Cell Line	embryonic stem cell
41	chr6:53722000-53723000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr6:53722000-53725000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
43	chr6:53722000-53748200	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr6:53722200-53722600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr6:53722200-53722600	Enhancers	iPS-20b Cell Line	embryonic stem cell
46	chr6:53722200-53722600	Flanking Active TSS	HUVEC	blood vessel
47	chr6:53722200-53722800	Enhancers	Adipose Nuclei	Adipose
48	chr6:53722200-53723000	Enhancers	Pancreas	Pancrea
49	chr6:53722400-53722600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
50	chr6:53722400-53722600	Flanking Active TSS	NHEK	skin

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