Variant report

Variant	rs12989754
Chromosome Location	chr2:63020970-63020971
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	chr2:63016408..63018608-chr2:63020047..63022575,3	MCF-7	breast:

Extended variants
information (count: 74 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10153716	0.95[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs1022110	0.87[CEU][hapmap];0.85[EUR][1000 genomes]
rs11682530	0.93[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11688816	0.93[ASW][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.88[YRI][hapmap];0.93[ASN][1000 genomes]
rs11893131	0.92[CEU][hapmap];0.96[YRI][hapmap]
rs12328837	0.93[JPT][hapmap]
rs12713467	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12713468	0.96[CEU][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12713469	0.85[CHB][hapmap];0.97[CHD][hapmap]
rs12994674	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13013218	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.88[LWK][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13398408	0.88[YRI][hapmap]
rs1386399	0.87[JPT][hapmap]
rs1420018	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1468748	0.85[ASW][hapmap];0.96[CEU][hapmap];0.91[GIH][hapmap];0.88[LWK][hapmap];0.93[TSI][hapmap];0.88[YRI][hapmap];0.81[EUR][1000 genomes]
rs1487074	0.93[JPT][hapmap]
rs1534418	0.87[JPT][hapmap]
rs1534420	0.87[JPT][hapmap]
rs1553832	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17027429	0.93[ASW][hapmap];0.96[CEU][hapmap];0.94[GIH][hapmap];0.91[LWK][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.88[YRI][hapmap];0.82[EUR][1000 genomes]
rs1828398	0.96[CEU][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs1872789	0.87[JPT][hapmap]
rs1872790	0.93[JPT][hapmap]
rs189671	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1906198	0.92[CEU][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs2058566	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2058567	0.82[EUR][1000 genomes]
rs2080227	0.88[YRI][hapmap]
rs2136737	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2204655	0.87[JPT][hapmap]
rs2204656	0.87[JPT][hapmap]
rs2215870	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2421816	0.92[CEU][hapmap];0.90[GIH][hapmap];0.89[TSI][hapmap]
rs2430388	0.93[ASW][hapmap];0.92[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.88[YRI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2539978	0.92[CEU][hapmap];0.88[GIH][hapmap];0.89[TSI][hapmap]
rs2539980	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap];0.84[ASN][1000 genomes]
rs2539985	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2539987	0.93[ASW][hapmap];0.92[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.87[YRI][hapmap]
rs2710637	0.85[ASW][hapmap];0.87[CEU][hapmap];0.87[GIH][hapmap];0.91[TSI][hapmap];0.83[YRI][hapmap]
rs2710638	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.88[ASN][1000 genomes]
rs2710639	0.88[CEU][hapmap]
rs2710640	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2710642	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2710647	0.90[CHB][hapmap];0.90[CHD][hapmap]
rs34104251	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs360797	0.86[ASW][hapmap];0.88[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.84[LWK][hapmap];0.81[TSI][hapmap];0.88[YRI][hapmap];0.80[EUR][1000 genomes]
rs360799	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs360800	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs360801	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.88[ASN][1000 genomes]
rs360804	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.88[ASN][1000 genomes]
rs360807	0.86[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.88[YRI][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs360808	0.84[CHB][hapmap];0.88[CHD][hapmap]
rs3927201	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4461246	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4671050	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4671051	0.89[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs4671448	0.90[CHB][hapmap]
rs4671450	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6545968	0.93[JPT][hapmap]
rs6545969	0.93[JPT][hapmap]
rs6545971	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6545972	0.93[ASW][hapmap];0.96[CEU][hapmap];0.94[GIH][hapmap];0.86[LWK][hapmap];0.82[MEX][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.82[EUR][1000 genomes]
rs6545973	0.92[CEU][hapmap];0.90[GIH][hapmap];0.91[TSI][hapmap]
rs6705835	0.93[JPT][hapmap]
rs6757128	0.93[JPT][hapmap]
rs7557501	0.93[ASW][hapmap];0.96[CEU][hapmap];0.94[GIH][hapmap];0.82[LWK][hapmap];0.98[TSI][hapmap];0.88[YRI][hapmap];0.82[EUR][1000 genomes]
rs7562149	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[GIH][hapmap];0.95[LWK][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs7562734	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7567923	0.93[ASW][hapmap];0.96[CEU][hapmap];0.94[GIH][hapmap];0.86[LWK][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.88[YRI][hapmap];0.82[EUR][1000 genomes]
rs7573756	0.86[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9678329	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9973612	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[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	nsv535767	chr2:62461582-63413596	Bivalent Enhancer Strong transcription Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS 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	50 gene(s)	inside rSNPs	diseases
2	esv3417336	chr2:62957866-63749654	Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:62982200-63033400	Weak transcription	Fetal Intestine Large	intestine
2	chr2:63010800-63032800	Weak transcription	Primary hematopoietic stem cells	blood
3	chr2:63013600-63022200	Weak transcription	HMEC	breast
4	chr2:63016400-63021800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr2:63017000-63021800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr2:63017000-63029000	Weak transcription	Ovary	ovary
7	chr2:63017000-63032600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr2:63017000-63033400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr2:63017000-63037400	Weak transcription	NHLF	lung
10	chr2:63017200-63021800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr2:63017400-63021800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr2:63017400-63022000	Weak transcription	Brain Hippocampus Middle	brain
13	chr2:63017400-63022200	Weak transcription	Fetal Lung	lung
14	chr2:63017400-63022400	Weak transcription	Adipose Nuclei	Adipose
15	chr2:63017400-63032800	Weak transcription	Stomach Smooth Muscle	stomach
16	chr2:63017400-63049400	Weak transcription	Fetal Heart	heart
17	chr2:63017600-63021600	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr2:63018000-63021600	Weak transcription	NHEK	skin
19	chr2:63018000-63021800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr2:63018200-63033400	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr2:63019200-63022600	Enhancers	HepG2	liver
22	chr2:63019600-63022000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr2:63019600-63022000	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr2:63019600-63043400	Weak transcription	Brain Angular Gyrus	brain
25	chr2:63020000-63021200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr2:63020000-63026600	Weak transcription	Dnd41	blood
27	chr2:63020400-63022000	Enhancers	A549	lung
28	chr2:63020400-63022200	Enhancers	NHDF-Ad	bronchial
29	chr2:63020400-63024800	Enhancers	Liver	Liver
30	chr2:63020600-63022800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr2:63020600-63023400	Enhancers	Colon Smooth Muscle	Colon
32	chr2:63020600-63023800	Enhancers	Rectal Smooth Muscle	rectum
33	chr2:63020600-63082000	Weak transcription	Pancreas	Pancrea
34	chr2:63020800-63021200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr2:63020800-63040200	Weak transcription	Left Ventricle	heart

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