Variant report

Variant	rs3003489
Chromosome Location	chr6:53690779-53690780
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 101 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs10948779	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11755346	0.85[EUR][1000 genomes]
rs13197492	0.85[ASN][1000 genomes]
rs13220665	0.94[CEU][hapmap];0.85[EUR][1000 genomes]
rs2745462	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2820215	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs2820216	1.00[CEU][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3000996	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3000997	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3000999	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3001000	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3001001	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3001002	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3001003	0.85[ASN][1000 genomes]
rs3001009	1.00[CEU][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3001010	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3003491	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3003493	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3003497	0.85[ASN][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[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[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4236115	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4265033	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4269375	0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs4276502	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4276503	0.83[ASN][1000 genomes]
rs4286781	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][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];0.96[EUR][1000 genomes]
rs4342426	0.83[ASN][1000 genomes]
rs4351263	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4382260	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4398733	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4437471	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4475321	0.85[ASN][1000 genomes]
rs4484515	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4489155	0.94[CEU][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4591854	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4615391	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4712048	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4712049	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4715424	0.94[CEU][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4715425	0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs4715426	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5001609	0.83[ASN][1000 genomes]
rs59641455	0.85[EUR][1000 genomes]
rs60035355	0.85[EUR][1000 genomes]
rs6458957	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6458958	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6458959	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6458960	0.85[ASN][1000 genomes]
rs6458961	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6458962	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6458965	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6458966	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6458969	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6458971	0.91[EUR][1000 genomes]
rs6458972	0.94[CEU][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.82[TSI][hapmap];0.91[YRI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6650996	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6899752	0.85[EUR][1000 genomes]
rs6901644	0.90[EUR][1000 genomes]
rs6920743	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6924025	0.93[CEU][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6925836	0.85[EUR][1000 genomes]
rs6926478	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6937901	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71555560	0.85[EUR][1000 genomes]
rs742524	1.00[CEU][hapmap]
rs7739965	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7753504	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7754791	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7759946	0.94[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs7762883	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7763081	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7763147	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7767443	1.00[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs7769893	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7774173	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9296719	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9296721	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9349686	0.83[ASN][1000 genomes]
rs9357774	0.83[ASN][1000 genomes]
rs9367542	0.85[ASN][1000 genomes]
rs9367544	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9370235	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9370239	0.85[ASW][hapmap];1.00[CEU][hapmap];0.91[GIH][hapmap];0.80[LWK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9382234	0.94[CEU][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9382237	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9382239	0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs9382250	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9395886	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]

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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3003489	POTEG	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53670800-53693200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr6:53676200-53697800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr6:53678600-53692200	Weak transcription	Esophagus	oesophagus
4	chr6:53680400-53691800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr6:53680400-53692400	Weak transcription	Pancreas	Pancrea
6	chr6:53680400-53721600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr6:53680600-53694400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr6:53684000-53691400	Weak transcription	Hela-S3	cervix
9	chr6:53684000-53692400	Weak transcription	Left Ventricle	heart
10	chr6:53684000-53694000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr6:53684000-53710200	Weak transcription	Primary T cells from cord blood	blood
12	chr6:53684600-53697000	Enhancers	Brain Substantia Nigra	brain
13	chr6:53687200-53692400	Weak transcription	Thymus	Thymus
14	chr6:53687400-53691600	Weak transcription	Right Atrium	heart
15	chr6:53687600-53692400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr6:53687600-53693000	Weak transcription	Stomach Smooth Muscle	stomach
17	chr6:53687600-53702000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr6:53687800-53690800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr6:53687800-53691200	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr6:53687800-53692200	Weak transcription	HSMM	muscle
21	chr6:53687800-53692800	Weak transcription	HSMMtube	muscle
22	chr6:53688000-53692000	Weak transcription	Brain Angular Gyrus	brain
23	chr6:53688000-53692400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr6:53688000-53694600	Weak transcription	Fetal Muscle Leg	muscle
25	chr6:53689400-53691400	Enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr6:53689400-53692000	Enhancers	Colonic Mucosa	Colon
27	chr6:53689400-53692000	Enhancers	Sigmoid Colon	Sigmoid Colon
28	chr6:53689400-53696400	Enhancers	Stomach Mucosa	stomach
29	chr6:53689400-53699400	Enhancers	Fetal Intestine Large	intestine
30	chr6:53689600-53694400	Enhancers	HepG2	liver
31	chr6:53689600-53695400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr6:53689800-53691000	Enhancers	Dnd41	blood
33	chr6:53689800-53691400	Enhancers	Rectal Smooth Muscle	rectum
34	chr6:53689800-53693400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr6:53689800-53693400	Enhancers	Small Intestine	intestine
36	chr6:53689800-53694000	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr6:53689800-53695000	Enhancers	HMEC	breast
38	chr6:53689800-53695200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr6:53689800-53697200	Enhancers	Colon Smooth Muscle	Colon
40	chr6:53690000-53695400	Enhancers	Brain Cingulate Gyrus	brain
41	chr6:53690000-53699000	Enhancers	Fetal Intestine Small	intestine
42	chr6:53690200-53691000	Enhancers	Brain Inferior Temporal Lobe	brain
43	chr6:53690200-53691000	Flanking Active TSS	Duodenum Mucosa	Duodenum
44	chr6:53690200-53691000	Enhancers	Fetal Thymus	thymus
45	chr6:53690200-53691400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
46	chr6:53690200-53695000	Enhancers	Brain Hippocampus Middle	brain
47	chr6:53690200-53695600	Enhancers	NHEK	skin
48	chr6:53690400-53690800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr6:53690400-53690800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr6:53690400-53690800	Active TSS	Rectal Mucosa Donor 29	rectum

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