Variant report

Variant	rs12712117
Chromosome Location	chr2:98389086-98389087
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:98381256..98384438-chr2:98386709..98392114,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000075568	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs10166513	0.94[ASN][1000 genomes]
rs10167772	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10168543	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10168709	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10169155	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10175129	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10180434	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10180837	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10183768	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10188497	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10188713	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10189414	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10191101	0.94[ASN][1000 genomes]
rs10192322	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10202138	0.94[ASN][1000 genomes]
rs10206684	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10208070	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10209970	0.88[ASN][1000 genomes]
rs10210520	1.00[ASN][1000 genomes]
rs10210880	0.88[ASN][1000 genomes]
rs11886417	0.88[ASN][1000 genomes]
rs11893437	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11894541	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11894895	1.00[ASN][1000 genomes]
rs11897301	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12712120	1.00[ASN][1000 genomes]
rs12712147	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12712162	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12712163	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12712172	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12991122	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12992955	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13000585	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13004862	0.89[ASN][1000 genomes]
rs13008678	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13008904	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13010004	1.00[ASN][1000 genomes]
rs13012645	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13387725	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13404788	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13427422	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1446327	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1503202	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1960329	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1982336	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2121271	1.00[ASN][1000 genomes]
rs2293679	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2305142	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34190123	0.94[ASN][1000 genomes]
rs34305873	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34414288	1.00[ASN][1000 genomes]
rs34469351	0.84[ASN][1000 genomes]
rs35185431	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35203092	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35402416	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35776557	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35807655	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35940587	0.88[ASN][1000 genomes]
rs36079497	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3821053	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55753459	0.94[ASN][1000 genomes]
rs6543088	0.91[ASN][1000 genomes]
rs6543111	0.97[ASN][1000 genomes]
rs6707719	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6707750	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6712078	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6718982	0.88[ASN][1000 genomes]
rs6721323	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6728312	1.00[ASN][1000 genomes]
rs6738401	0.94[ASN][1000 genomes]
rs6751727	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6755021	0.94[ASN][1000 genomes]
rs6756969	0.88[ASN][1000 genomes]
rs6760008	1.00[ASN][1000 genomes]
rs68115667	0.88[ASN][1000 genomes]
rs6875	0.88[ASN][1000 genomes]
rs71429373	0.94[ASN][1000 genomes]
rs718159	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7557495	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7570009	1.00[ASN][1000 genomes]
rs7578638	0.88[ASN][1000 genomes]
rs7582298	0.94[ASN][1000 genomes]
rs7588227	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7593290	1.00[ASN][1000 genomes]
rs7594928	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7595039	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7599043	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7605288	0.88[ASN][1000 genomes]
rs9784011	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9808558	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9973490	0.85[ASN][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	nsv531382	chr2:98250628-98457616	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:98352200-98398800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr2:98366200-98400000	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr2:98368000-98393800	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr2:98368600-98413000	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr2:98369600-98398800	Strong transcription	Fetal Muscle Leg	muscle
6	chr2:98370200-98392600	Strong transcription	Cortex derived primary cultured neurospheres	brain
7	chr2:98370600-98392400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:98370600-98393800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr2:98370600-98407600	Weak transcription	HUVEC	blood vessel
10	chr2:98371200-98398600	Strong transcription	Primary B cells from cord blood	blood
11	chr2:98373800-98390400	Weak transcription	K562	blood
12	chr2:98377200-98394400	Strong transcription	Rectal Mucosa Donor 31	rectum
13	chr2:98377400-98408000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr2:98377400-98410600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr2:98378200-98389600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr2:98378600-98421400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr2:98380800-98393800	Strong transcription	Primary neutrophils fromperipheralblood	blood
18	chr2:98381400-98397600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr2:98382600-98389600	Weak transcription	Gastric	stomach
20	chr2:98382600-98391600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr2:98382800-98389400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr2:98382800-98398600	Weak transcription	Small Intestine	intestine
23	chr2:98382800-98419800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr2:98383000-98390000	Weak transcription	Brain Angular Gyrus	brain
25	chr2:98383000-98390200	Weak transcription	Brain Substantia Nigra	brain
26	chr2:98383000-98408600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr2:98383200-98389400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr2:98383200-98389600	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr2:98383200-98389800	Weak transcription	Colon Smooth Muscle	Colon
30	chr2:98383200-98408800	Weak transcription	Fetal Brain Male	brain
31	chr2:98383200-98420200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr2:98383400-98389600	Weak transcription	Dnd41	blood
33	chr2:98383400-98389600	Weak transcription	HSMM	muscle
34	chr2:98383400-98391600	Weak transcription	Fetal Kidney	kidney
35	chr2:98383400-98405600	Weak transcription	A549	lung
36	chr2:98383600-98391600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr2:98383800-98389400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr2:98384000-98398800	Weak transcription	Stomach Mucosa	stomach
39	chr2:98384400-98389400	Weak transcription	Pancreas	Pancrea
40	chr2:98384400-98389600	Weak transcription	Aorta	Aorta
41	chr2:98384400-98390800	Weak transcription	NHLF	lung
42	chr2:98385400-98392600	Strong transcription	Fetal Lung	lung
43	chr2:98385400-98399200	Strong transcription	Primary B cells from peripheral blood	blood
44	chr2:98385600-98389400	Weak transcription	Right Ventricle	heart
45	chr2:98385800-98392400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr2:98385800-98398800	Strong transcription	Fetal Stomach	stomach
47	chr2:98386000-98392400	Strong transcription	Placenta	Placenta
48	chr2:98386000-98392400	Strong transcription	HMEC	breast
49	chr2:98386000-98392600	Strong transcription	Primary T cells from cord blood	blood
50	chr2:98386000-98398800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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