Variant report

Variant	rs10880762
Chromosome Location	chr12:45635988-45635989
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	chr12:45626376..45630112-chr12:45635630..45638658,4	MCF-7	breast:

Extended variants
information (count: 104 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs1015626	0.82[CHB][hapmap];0.85[JPT][hapmap];0.81[AMR][1000 genomes]
rs10437984	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10459293	0.89[CEU][hapmap];0.91[EUR][1000 genomes]
rs10459294	0.89[CEU][hapmap];0.91[EUR][1000 genomes]
rs10492284	0.89[CEU][hapmap];0.91[EUR][1000 genomes]
rs10748412	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10785556	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10785557	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10785566	0.82[CHB][hapmap];0.85[JPT][hapmap];0.81[AMR][1000 genomes]
rs10880755	0.85[JPT][hapmap];0.86[AMR][1000 genomes]
rs10880756	0.86[AMR][1000 genomes]
rs10880760	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10880761	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10880763	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10880764	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10880771	0.81[AMR][1000 genomes]
rs11182903	0.81[EUR][1000 genomes]
rs11182904	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11182905	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11182908	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11182912	0.89[EUR][1000 genomes]
rs11182913	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11182916	0.89[CEU][hapmap];0.91[EUR][1000 genomes]
rs11182917	0.91[EUR][1000 genomes]
rs11182918	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11182919	0.89[CEU][hapmap];0.91[EUR][1000 genomes]
rs11182921	0.91[EUR][1000 genomes]
rs11182922	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11182923	0.91[EUR][1000 genomes]
rs11182927	0.89[CEU][hapmap];0.91[EUR][1000 genomes]
rs11182931	0.89[CEU][hapmap];0.91[EUR][1000 genomes]
rs11182935	0.91[EUR][1000 genomes]
rs11182936	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11182938	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11182939	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11182940	0.91[EUR][1000 genomes]
rs11182941	0.91[EUR][1000 genomes]
rs11182942	0.81[EUR][1000 genomes]
rs11182943	0.91[EUR][1000 genomes]
rs11182944	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11182946	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11182947	0.89[EUR][1000 genomes]
rs11182949	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11561532	0.91[EUR][1000 genomes]
rs11610233	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11611509	0.81[EUR][1000 genomes]
rs11612203	0.91[EUR][1000 genomes]
rs11612233	0.89[CEU][hapmap];0.91[EUR][1000 genomes]
rs11615850	0.91[EUR][1000 genomes]
rs12226944	0.82[EUR][1000 genomes]
rs12227678	0.89[CEU][hapmap];0.91[EUR][1000 genomes]
rs12228733	0.81[EUR][1000 genomes]
rs12230322	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12231753	0.90[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12299174	0.81[EUR][1000 genomes]
rs12320168	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12320437	0.89[EUR][1000 genomes]
rs12322087	0.81[EUR][1000 genomes]
rs12814332	0.89[EUR][1000 genomes]
rs12815115	0.91[EUR][1000 genomes]
rs12815577	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12822746	0.91[EUR][1000 genomes]
rs12828052	0.85[EUR][1000 genomes]
rs1399721	0.81[AMR][1000 genomes]
rs17095551	0.91[EUR][1000 genomes]
rs17095557	0.89[CEU][hapmap];0.91[EUR][1000 genomes]
rs1913692	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs2052602	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2052603	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2408184	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2408185	0.89[CEU][hapmap];0.91[EUR][1000 genomes]
rs34024171	0.91[EUR][1000 genomes]
rs35054776	0.89[CEU][hapmap];0.91[EUR][1000 genomes]
rs35588430	0.81[EUR][1000 genomes]
rs35660715	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3759077	0.91[EUR][1000 genomes]
rs3759080	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3759081	0.91[EUR][1000 genomes]
rs3759082	0.89[CEU][hapmap];0.87[EUR][1000 genomes]
rs3782131	0.89[CEU][hapmap];0.91[EUR][1000 genomes]
rs4768085	0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4768601	0.83[CHB][hapmap];0.80[JPT][hapmap]
rs57797434	0.91[EUR][1000 genomes]
rs58444879	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs61923810	0.91[EUR][1000 genomes]
rs61923825	0.91[EUR][1000 genomes]
rs61923830	0.91[EUR][1000 genomes]
rs7135988	0.86[JPT][hapmap];0.81[AMR][1000 genomes]
rs7136368	0.81[AMR][1000 genomes]
rs7138247	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs7138983	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs728590	0.83[CHB][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes]
rs7304481	0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7307262	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs7309615	0.85[JPT][hapmap];0.81[AMR][1000 genomes]
rs7956033	0.94[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7963038	1.00[CEU][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7963057	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7964635	0.82[ASN][1000 genomes]
rs7965430	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs7971900	0.85[JPT][hapmap];0.80[AMR][1000 genomes]
rs929903	0.81[AMR][1000 genomes]
rs9739519	1.00[EUR][1000 genomes];0.99[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	nsv1050923	chr12:45581310-45808289	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:45613800-45638000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr12:45613800-45638200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr12:45614000-45637600	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr12:45614400-45639600	Weak transcription	Dnd41	blood
5	chr12:45614400-45650200	Weak transcription	Primary T cells from cord blood	blood
6	chr12:45627400-45650600	Weak transcription	Primary B cells from cord blood	blood
7	chr12:45629200-45636200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr12:45629400-45636000	Weak transcription	Primary hematopoietic stem cells	blood
9	chr12:45629800-45636000	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr12:45629800-45637600	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr12:45629800-45638000	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr12:45629800-45638000	Weak transcription	Liver	Liver
13	chr12:45629800-45638400	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr12:45629800-45638400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr12:45629800-45638600	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr12:45629800-45638600	Weak transcription	Spleen	Spleen
17	chr12:45629800-45640000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr12:45629800-45640200	Weak transcription	Gastric	stomach
19	chr12:45629800-45640400	Weak transcription	Ovary	ovary
20	chr12:45629800-45641400	Weak transcription	Left Ventricle	heart
21	chr12:45629800-45642600	Weak transcription	Brain Substantia Nigra	brain
22	chr12:45629800-45642600	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr12:45629800-45651000	Weak transcription	K562	blood
24	chr12:45629800-45651400	Weak transcription	Fetal Intestine Large	intestine
25	chr12:45629800-45652400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr12:45630000-45636800	Weak transcription	GM12878-XiMat	blood
27	chr12:45630000-45638200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr12:45630000-45638200	Weak transcription	Duodenum Mucosa	Duodenum
29	chr12:45630000-45638200	Weak transcription	Stomach Smooth Muscle	stomach
30	chr12:45630000-45638200	Weak transcription	NHDF-Ad	bronchial
31	chr12:45630000-45638400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr12:45630000-45638600	Weak transcription	Placenta	Placenta
33	chr12:45630000-45640200	Weak transcription	Fetal Lung	lung
34	chr12:45630000-45647800	Weak transcription	Right Ventricle	heart
35	chr12:45630000-45648600	Weak transcription	NHEK	skin
36	chr12:45630000-45651000	Weak transcription	Fetal Muscle Leg	muscle
37	chr12:45630000-45651000	Weak transcription	HepG2	liver
38	chr12:45630000-45653200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr12:45630200-45637800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr12:45630200-45638200	Weak transcription	A549	lung
41	chr12:45630200-45638400	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr12:45630200-45638400	Weak transcription	Rectal Smooth Muscle	rectum
43	chr12:45630400-45641200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr12:45633800-45637600	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr12:45635200-45636200	Enhancers	Placenta Amnion	Placenta Amnion
46	chr12:45635200-45637200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr12:45635600-45636000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr12:45635600-45636000	Strong transcription	Fetal Muscle Trunk	muscle
49	chr12:45635600-45636200	Enhancers	ES-I3 Cell Line	embryonic stem cell
50	chr12:45635600-45636200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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