Variant report

Variant	rs12505249
Chromosome Location	chr4:26622610-26622611
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:26621660..26623538-chr4:26623814..26625378,2	MCF-7	breast:

Extended variants
information (count: 94 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10000211	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10939124	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10939128	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10939132	0.84[EUR][1000 genomes]
rs10939134	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs10939135	0.83[EUR][1000 genomes]
rs1129230	0.92[CEU][hapmap];0.93[GIH][hapmap];1.00[TSI][hapmap]
rs11721891	0.96[CEU][hapmap];0.98[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs11724595	0.81[EUR][1000 genomes]
rs11733702	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11931159	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs11937465	0.81[EUR][1000 genomes]
rs11942145	0.92[CEU][hapmap]
rs11944010	0.81[EUR][1000 genomes]
rs12498454	0.84[EUR][1000 genomes]
rs12501439	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12504472	0.84[EUR][1000 genomes]
rs12507314	0.92[CEU][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];0.81[EUR][1000 genomes]
rs12510371	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12510995	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12640312	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12640951	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12644574	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs12647180	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12650361	1.00[CEU][hapmap];0.98[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs13105574	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13111381	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13111922	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13121299	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13121378	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13125612	0.96[CEU][hapmap];0.98[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs13131355	0.82[EUR][1000 genomes]
rs13136955	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13138699	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13138712	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13146364	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs13146615	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1565303	0.96[CEU][hapmap];0.97[EUR][1000 genomes]
rs1565304	0.96[EUR][1000 genomes]
rs1619573	0.96[CEU][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs1641562	0.89[CEU][hapmap];0.90[EUR][1000 genomes]
rs1861470	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs2111006	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2309413	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs260934	0.92[EUR][1000 genomes]
rs260935	0.92[EUR][1000 genomes]
rs260937	0.95[EUR][1000 genomes]
rs260939	0.92[EUR][1000 genomes]
rs260946	0.92[EUR][1000 genomes]
rs260948	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs260950	1.00[CEU][hapmap];0.98[GIH][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs260952	0.95[EUR][1000 genomes]
rs260956	0.97[EUR][1000 genomes]
rs260958	1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs260959	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs260960	0.97[EUR][1000 genomes]
rs2908823	0.95[EUR][1000 genomes]
rs34010107	0.84[EUR][1000 genomes]
rs34241157	0.83[EUR][1000 genomes]
rs34832881	0.94[EUR][1000 genomes]
rs35232657	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35445672	0.92[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs35654367	0.81[EUR][1000 genomes]
rs4234981	0.81[EUR][1000 genomes]
rs4321621	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs4355378	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4365714	0.84[EUR][1000 genomes]
rs4437235	0.96[CEU][hapmap];0.98[GIH][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs4467548	0.84[EUR][1000 genomes]
rs4527463	0.92[CEU][hapmap];0.98[GIH][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs4588446	0.95[GIH][hapmap];1.00[TSI][hapmap]
rs4590010	0.96[CEU][hapmap];0.98[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs4692549	0.89[GIH][hapmap];0.83[TSI][hapmap]
rs4692551	0.85[EUR][1000 genomes]
rs56150091	0.81[EUR][1000 genomes]
rs60503601	0.84[EUR][1000 genomes]
rs60915838	0.83[EUR][1000 genomes]
rs61690082	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62409934	0.94[EUR][1000 genomes]
rs62412678	0.83[EUR][1000 genomes]
rs6448458	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67655603	0.97[EUR][1000 genomes]
rs6821370	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6858652	0.92[CEU][hapmap];0.98[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs7655144	0.84[EUR][1000 genomes]
rs7657453	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7658999	0.89[CEU][hapmap];0.98[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs7672267	0.81[EUR][1000 genomes]
rs7677353	0.84[EUR][1000 genomes]
rs7683324	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs7687087	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9790514	0.82[EUR][1000 genomes]
rs9790776	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv966489	chr4:26600972-26641744	Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:26606400-26656600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr4:26608800-26643600	Weak transcription	Fetal Heart	heart
3	chr4:26609000-26625400	Weak transcription	Colon Smooth Muscle	Colon
4	chr4:26609600-26640000	Weak transcription	Left Ventricle	heart
5	chr4:26609600-26649400	Weak transcription	Psoas Muscle	Psoas
6	chr4:26609800-26632400	Weak transcription	Primary B cells from cord blood	blood
7	chr4:26611200-26639600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr4:26611400-26624600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr4:26613200-26634400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr4:26613400-26639600	Weak transcription	Fetal Brain Female	brain
11	chr4:26613800-26634400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr4:26613800-26657200	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr4:26614000-26624400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr4:26614000-26633400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr4:26614000-26638800	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr4:26614000-26640600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr4:26614200-26641400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr4:26615000-26642000	Weak transcription	Fetal Intestine Small	intestine
19	chr4:26615200-26634200	Weak transcription	Fetal Muscle Leg	muscle
20	chr4:26615400-26638800	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr4:26615600-26641800	Weak transcription	Brain Germinal Matrix	brain
22	chr4:26615600-26642000	Weak transcription	Aorta	Aorta
23	chr4:26615800-26624400	Weak transcription	Dnd41	blood
24	chr4:26615800-26635000	Weak transcription	Thymus	Thymus
25	chr4:26615800-26640200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr4:26616600-26622800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr4:26616600-26628400	Strong transcription	Fetal Thymus	thymus
28	chr4:26616600-26639400	Weak transcription	Adipose Nuclei	Adipose
29	chr4:26616600-26641800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr4:26616600-26641800	Weak transcription	Primary B cells from peripheral blood	blood
31	chr4:26616600-26662600	Weak transcription	Stomach Smooth Muscle	stomach
32	chr4:26617200-26642200	Weak transcription	Brain Angular Gyrus	brain
33	chr4:26618000-26640400	Weak transcription	NH-A	brain
34	chr4:26618200-26634800	Weak transcription	Ovary	ovary
35	chr4:26618200-26638600	Weak transcription	Primary T cells fromperipheralblood	blood
36	chr4:26618200-26639800	Weak transcription	Fetal Brain Male	brain
37	chr4:26618200-26640000	Weak transcription	Fetal Intestine Large	intestine
38	chr4:26618200-26657200	Weak transcription	Pancreas	Pancrea
39	chr4:26618400-26624800	Weak transcription	HUVEC	blood vessel
40	chr4:26618400-26639200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr4:26618400-26642000	Weak transcription	Esophagus	oesophagus
42	chr4:26618600-26626400	Weak transcription	Fetal Stomach	stomach
43	chr4:26618600-26640000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr4:26618800-26626400	Weak transcription	Rectal Smooth Muscle	rectum
45	chr4:26618800-26627400	Weak transcription	Fetal Kidney	kidney
46	chr4:26619600-26639600	Weak transcription	HSMMtube	muscle
47	chr4:26619600-26645600	Weak transcription	Spleen	Spleen
48	chr4:26619800-26634600	Weak transcription	Fetal Lung	lung
49	chr4:26619800-26640000	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr4:26620000-26634400	Weak transcription	Primary T cells from cord blood	blood

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