Variant report

Variant	rs12772552
Chromosome Location	chr10:89562046-89562047
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	chr10:89560023..89562647-chr10:89574852..89577669,2	MCF-7	breast:

Extended variants
information (count: 114 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:112)

rs_ID	r²[population]
rs10082347	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1051441	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10887748	0.89[YRI][hapmap]
rs10887749	0.89[YRI][hapmap]
rs10887750	0.89[YRI][hapmap]
rs10887753	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11202526	0.89[YRI][hapmap]
rs11202527	0.89[YRI][hapmap]
rs11202536	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11202538	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11202553	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11202557	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11202563	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11202564	0.88[CEU][hapmap]
rs11202565	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11202568	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11202571	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11498630	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11812787	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11816798	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11817759	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11818430	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12247482	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12253113	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12413371	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12570131	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12570639	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12571331	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12572346	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12572581	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12573160	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12573349	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12762731	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12765184	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12765681	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12768487	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12769214	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12769771	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12770433	0.94[EUR][1000 genomes]
rs12770684	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12771188	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12771844	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12773536	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12775017	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12775041	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[EUR][1000 genomes]
rs12776656	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12778199	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs12779667	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12779915	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12780234	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12780237	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12781171	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12782128	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12782235	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12782454	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12783598	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17096702	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1819162	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs1819163	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1853167	0.88[CEU][hapmap]
rs1923260	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1923261	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1923262	0.91[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1960047	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1993845	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2038554	0.95[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2057358	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2067661	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2306157	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34325090	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34466534	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34559481	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34878240	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35254974	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35388513	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35662941	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35814940	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3740278	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3816651	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4443987	0.93[YRI][hapmap];0.96[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs4933461	0.89[YRI][hapmap]
rs4934363	0.89[YRI][hapmap]
rs4934364	0.89[YRI][hapmap]
rs4934366	0.89[YRI][hapmap]
rs4934367	0.89[YRI][hapmap]
rs4934369	0.85[AFR][1000 genomes]
rs6586102	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs66863455	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7068497	0.87[CEU][hapmap]
rs7073644	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7085412	0.81[EUR][1000 genomes]
rs7090088	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7090432	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7096449	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7098653	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7480	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7481	0.95[CEU][hapmap];0.92[YRI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7898915	0.87[CEU][hapmap]
rs7901767	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7904344	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7905932	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7908203	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7910692	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7913763	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7920554	0.89[YRI][hapmap]
rs7920778	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7920910	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7921017	0.88[YRI][hapmap]
rs7921889	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9651491	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9663978	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9664653	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][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	nsv518233	chr10:89512839-89584002	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv1041462	chr10:89518729-89584284	Strong transcription Flanking Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:89473000-89577200	Weak transcription	Gastric	stomach
2	chr10:89495000-89576400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr10:89495200-89577400	Weak transcription	Spleen	Spleen
4	chr10:89511000-89576800	Weak transcription	Colonic Mucosa	Colon
5	chr10:89513400-89577000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr10:89520600-89575600	Weak transcription	Stomach Mucosa	stomach
7	chr10:89523400-89562800	Weak transcription	K562	blood
8	chr10:89527400-89575000	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr10:89530800-89575800	Weak transcription	Brain Cingulate Gyrus	brain
10	chr10:89536200-89574600	Weak transcription	Brain Anterior Caudate	brain
11	chr10:89537000-89576400	Weak transcription	HSMMtube	muscle
12	chr10:89540200-89562800	Weak transcription	Fetal Heart	heart
13	chr10:89540800-89563000	Weak transcription	Ovary	ovary
14	chr10:89541800-89575000	Weak transcription	Right Ventricle	heart
15	chr10:89542000-89571200	Weak transcription	Brain Hippocampus Middle	brain
16	chr10:89543000-89571400	Weak transcription	Rectal Smooth Muscle	rectum
17	chr10:89543200-89563200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr10:89543200-89572200	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr10:89543400-89577200	Weak transcription	Aorta	Aorta
20	chr10:89547000-89563800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr10:89548200-89574800	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr10:89549400-89575400	Weak transcription	Brain Angular Gyrus	brain
23	chr10:89550000-89572200	Weak transcription	HUVEC	blood vessel
24	chr10:89552600-89566200	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr10:89552800-89571400	Weak transcription	NHEK	skin
26	chr10:89553000-89570000	Weak transcription	HMEC	breast
27	chr10:89553200-89565800	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr10:89553200-89569800	Weak transcription	Stomach Smooth Muscle	stomach
29	chr10:89554400-89570800	Weak transcription	Esophagus	oesophagus
30	chr10:89554400-89577200	Weak transcription	Pancreas	Pancrea
31	chr10:89555400-89564600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr10:89556200-89573800	Strong transcription	HSMM	muscle
33	chr10:89556400-89565800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr10:89556600-89569200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr10:89557000-89575000	Weak transcription	Adipose Nuclei	Adipose
36	chr10:89557000-89575800	Weak transcription	NH-A	brain
37	chr10:89557400-89563400	Weak transcription	Brain Germinal Matrix	brain
38	chr10:89557600-89567000	Weak transcription	Placenta	Placenta
39	chr10:89557800-89567200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr10:89558000-89569200	Weak transcription	Fetal Stomach	stomach
41	chr10:89558000-89573400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr10:89558200-89564600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr10:89558200-89565200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr10:89558600-89563000	Weak transcription	Hela-S3	cervix
45	chr10:89558800-89564200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
46	chr10:89558800-89565200	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
47	chr10:89558800-89570400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr10:89559000-89562400	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
49	chr10:89559000-89563600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr10:89559000-89563800	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell

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