Variant report

Variant	rs66590925
Chromosome Location	chr12:1851286-1851287
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	chr12:1814200..1816471-chr12:1849026..1851387,2	MCF-7	breast:
2	chr12:1847981..1850303-chr12:1850538..1853225,2	K562	blood:

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1029629	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10773982	0.81[AMR][1000 genomes]
rs10773986	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10848551	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10848552	0.92[ASN][1000 genomes]
rs10848553	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10848558	0.87[AMR][1000 genomes]
rs10848566	0.82[ASN][1000 genomes]
rs10848569	0.91[AMR][1000 genomes]
rs11061919	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11061920	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11061921	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11061923	0.84[AMR][1000 genomes]
rs11061924	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11061925	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11061927	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11061937	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11061940	0.87[AMR][1000 genomes]
rs11061956	0.82[ASN][1000 genomes]
rs11061957	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11061962	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11061968	0.91[AMR][1000 genomes]
rs11061974	0.90[AMR][1000 genomes]
rs1136213	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11832817	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12230579	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12231894	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12342	0.86[AMR][1000 genomes]
rs12581815	0.83[ASN][1000 genomes]
rs12582624	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12810020	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12812707	0.91[AMR][1000 genomes]
rs12813694	0.91[AMR][1000 genomes]
rs12828908	0.91[AMR][1000 genomes]
rs12831353	0.91[AMR][1000 genomes]
rs2058034	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2058035	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2240613	0.88[AMR][1000 genomes]
rs2286385	0.88[AMR][1000 genomes]
rs2370055	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34375871	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3809266	0.88[AMR][1000 genomes]
rs4766413	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6489320	0.82[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs6489323	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6489324	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7132033	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs71454839	0.81[ASN][1000 genomes]
rs7297509	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7313760	0.91[AMR][1000 genomes]
rs7975826	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7978818	0.87[AMR][1000 genomes]
rs929434	0.91[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042863	chr12:1163817-1902302	Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv541345	chr12:1163817-1902302	Strong transcription Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv832304	chr12:1710249-1868642	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv832305	chr12:1769852-1936054	Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv948480	chr12:1776217-2284333	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
6	nsv832306	chr12:1847726-2001308	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:1816200-1857800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr12:1816200-1866400	Weak transcription	Esophagus	oesophagus
3	chr12:1816200-1897400	Weak transcription	Aorta	Aorta
4	chr12:1817000-1856600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr12:1823000-1866600	Weak transcription	Gastric	stomach
6	chr12:1824000-1866600	Weak transcription	HSMM	muscle
7	chr12:1825200-1855400	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr12:1826000-1885400	Weak transcription	NH-A	brain
9	chr12:1828600-1855800	Weak transcription	Fetal Intestine Large	intestine
10	chr12:1831400-1857800	Weak transcription	Lung	lung
11	chr12:1836800-1855400	Weak transcription	Primary hematopoietic stem cells	blood
12	chr12:1837000-1861600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr12:1837200-1855400	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr12:1840800-1852000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr12:1840800-1854000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr12:1840800-1855600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr12:1841800-1851400	Weak transcription	Brain Angular Gyrus	brain
18	chr12:1842400-1854200	Weak transcription	Dnd41	blood
19	chr12:1845600-1885200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr12:1846000-1851800	Enhancers	Skeletal Muscle Male	skeletal muscle
21	chr12:1846000-1852200	Enhancers	HepG2	liver
22	chr12:1846600-1851400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr12:1847200-1851400	Weak transcription	Brain Anterior Caudate	brain
24	chr12:1847200-1851800	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr12:1847600-1854200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr12:1847600-1857800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr12:1847600-1863800	Weak transcription	Ovary	ovary
28	chr12:1847600-1885200	Weak transcription	Right Atrium	heart
29	chr12:1849200-1851600	Enhancers	Primary T killer memory cells from peripheral blood	blood
30	chr12:1849200-1851800	Enhancers	Adipose Nuclei	Adipose
31	chr12:1849200-1851800	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr12:1849400-1851400	Enhancers	Primary T helper naive cells from peripheral blood	blood
33	chr12:1849400-1851400	Enhancers	Fetal Heart	heart
34	chr12:1849400-1851400	Enhancers	Hela-S3	cervix
35	chr12:1849400-1851600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
36	chr12:1849400-1851800	Enhancers	Primary neutrophils fromperipheralblood	blood
37	chr12:1849400-1851800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
38	chr12:1849400-1851800	Enhancers	Thymus	Thymus
39	chr12:1849400-1852800	Enhancers	Brain Hippocampus Middle	brain
40	chr12:1849600-1852400	Enhancers	Brain Substantia Nigra	brain
41	chr12:1849800-1851400	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr12:1849800-1855400	Weak transcription	Left Ventricle	heart
43	chr12:1849800-1868400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr12:1849800-1868800	Weak transcription	Pancreas	Pancrea
45	chr12:1849800-1905600	Weak transcription	Small Intestine	intestine
46	chr12:1850000-1851400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr12:1850000-1851600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
48	chr12:1850000-1851600	Enhancers	Primary B cells from cord blood	blood
49	chr12:1850000-1856800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr12:1850000-1866600	Weak transcription	Fetal Lung	lung

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