Variant report

Variant	rs12712162
Chromosome Location	chr2:98460742-98460743
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	chr2:98460157..98461812-chr2:98473949..98476657,2	MCF-7	breast:

Extended variants
information (count: 110 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs10166513	0.94[ASN][1000 genomes]
rs10167772	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10168543	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10168709	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10169155	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10175129	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10176826	0.96[CEU][hapmap];0.85[CHB][hapmap];0.82[EUR][1000 genomes]
rs10180434	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10180837	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10183768	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10184393	0.86[EUR][1000 genomes]
rs10184457	0.96[CEU][hapmap];0.85[CHB][hapmap];0.96[LWK][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs10184552	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs10188497	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10188713	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10189414	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10191101	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10191483	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs10192322	0.85[CEU][hapmap];0.82[CHB][hapmap];0.84[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs10202138	0.94[ASN][1000 genomes]
rs10206684	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10208070	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10209970	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10210299	0.81[EUR][1000 genomes]
rs10210520	0.88[ASN][1000 genomes]
rs10210880	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1024086	1.00[CHB][hapmap]
rs11886417	0.88[ASN][1000 genomes]
rs11893437	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11894541	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11894895	0.88[ASN][1000 genomes]
rs11895170	0.96[CEU][hapmap];0.85[CHB][hapmap];0.81[EUR][1000 genomes]
rs11897301	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12712117	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12712120	0.88[ASN][1000 genomes]
rs12712147	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12712163	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12712172	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12992955	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13000585	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13008678	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13008904	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13010004	0.88[ASN][1000 genomes]
rs13012645	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13387725	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13404788	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13427422	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1446327	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1503202	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1960329	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1982336	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2121271	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2293679	0.96[CEU][hapmap];0.85[CHB][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2305142	0.81[CEU][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs34190123	0.94[ASN][1000 genomes]
rs34305873	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34414288	0.88[ASN][1000 genomes]
rs34469351	0.85[ASN][1000 genomes]
rs35185431	0.84[AFR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35203092	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35402416	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35776557	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35807655	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35940587	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs36079497	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3821053	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55753459	0.94[ASN][1000 genomes]
rs55817781	0.81[EUR][1000 genomes]
rs6543088	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs6543111	0.85[ASN][1000 genomes]
rs6707719	0.96[CEU][hapmap];0.85[CHB][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6707750	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6712078	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6713504	0.83[EUR][1000 genomes]
rs6718982	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6721323	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[MKK][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6728312	0.88[ASN][1000 genomes]
rs6736735	0.81[CEU][hapmap]
rs6738401	0.94[ASN][1000 genomes]
rs6751727	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6755021	0.94[ASN][1000 genomes]
rs6756969	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6760008	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs68115667	0.88[ASN][1000 genomes]
rs6875	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs71429373	0.94[ASN][1000 genomes]
rs718159	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7557495	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7570009	0.88[ASN][1000 genomes]
rs7578638	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7582298	0.94[ASN][1000 genomes]
rs7588227	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7591374	0.86[EUR][1000 genomes]
rs7593290	0.88[ASN][1000 genomes]
rs7594928	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7595039	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7599043	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7605288	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9784011	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9808558	0.96[CEU][hapmap];0.85[CHB][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9973490	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526360	chr2:98403683-98814054	Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv521568	chr2:98403683-98826203	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1004220	chr2:98423421-98816010	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1007259	chr2:98429744-98818080	Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv535832	chr2:98429744-98818080	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv1009218	chr2:98442640-98816010	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv1003925	chr2:98442640-98821102	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv999442	chr2:98448732-98816010	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv1013902	chr2:98454309-98818080	ZNF genes & repeats Weak transcription Bivalent/Poised TSS Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:98406400-98469200	Weak transcription	A549	lung
2	chr2:98409400-98484200	Weak transcription	HUVEC	blood vessel
3	chr2:98409800-98485000	Weak transcription	Hela-S3	cervix
4	chr2:98424000-98475000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr2:98424200-98461600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr2:98425600-98461000	Weak transcription	Brain Germinal Matrix	brain
7	chr2:98428000-98466600	Weak transcription	K562	blood
8	chr2:98428600-98461200	Weak transcription	Fetal Brain Male	brain
9	chr2:98428600-98464600	Weak transcription	HSMMtube	muscle
10	chr2:98428800-98485000	Weak transcription	NHLF	lung
11	chr2:98429000-98470600	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr2:98430000-98467800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr2:98431000-98466400	Weak transcription	NH-A	brain
14	chr2:98434200-98484000	Weak transcription	NHDF-Ad	bronchial
15	chr2:98434400-98466400	Weak transcription	Brain Substantia Nigra	brain
16	chr2:98434400-98485800	Weak transcription	Lung	lung
17	chr2:98446000-98475000	Weak transcription	Gastric	stomach
18	chr2:98447400-98465400	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr2:98447600-98461200	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr2:98447800-98461200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr2:98447800-98466200	Weak transcription	Psoas Muscle	Psoas
22	chr2:98447800-98479600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr2:98447800-98502800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr2:98448000-98461200	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr2:98449600-98482000	Weak transcription	Fetal Kidney	kidney
26	chr2:98451800-98466200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr2:98457000-98466400	Weak transcription	Osteobl	bone
28	chr2:98457000-98477400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr2:98457000-98477400	Weak transcription	Esophagus	oesophagus
30	chr2:98457000-98478000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr2:98457000-98485600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr2:98457200-98466200	Weak transcription	Brain Cingulate Gyrus	brain
33	chr2:98457200-98467600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr2:98457200-98485800	Weak transcription	Brain Anterior Caudate	brain
35	chr2:98457400-98461200	Weak transcription	Fetal Brain Female	brain
36	chr2:98457400-98466600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr2:98457400-98485800	Weak transcription	Aorta	Aorta
38	chr2:98457600-98461000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr2:98457600-98461000	Weak transcription	Right Ventricle	heart
40	chr2:98457600-98461200	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr2:98457600-98465800	Weak transcription	Brain Angular Gyrus	brain
42	chr2:98457600-98468200	Weak transcription	Fetal Thymus	thymus
43	chr2:98457600-98469000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr2:98457600-98475000	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr2:98457600-98475000	Weak transcription	Fetal Stomach	stomach
46	chr2:98457600-98475000	Weak transcription	Pancreas	Pancrea
47	chr2:98457600-98475000	Weak transcription	Stomach Smooth Muscle	stomach
48	chr2:98457600-98475000	Weak transcription	Spleen	Spleen
49	chr2:98457600-98475200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr2:98457600-98477600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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