Variant report

Variant	rs12230579
Chromosome Location	chr12:1817073-1817074
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:1817051..1819015-chr12:1820770..1822956,2	K562	blood:
2	chr12:1815296..1817227-chr12:1871744..1873347,2	MCF-7	breast:
3	chr12:1815063..1817215-chr12:1824872..1827970,3	K562	blood:
4	chr12:1799438..1802227-chr12:1816513..1818304,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000006831	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1029629	0.82[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10773986	0.90[CEU][hapmap];0.88[YRI][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10848551	1.00[CEU][hapmap];0.95[CHB][hapmap];0.84[JPT][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10848552	0.94[ASN][1000 genomes]
rs10848553	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10848558	0.85[AMR][1000 genomes]
rs10848566	0.81[ASN][1000 genomes]
rs10848569	0.88[AMR][1000 genomes]
rs11061919	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11061920	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11061921	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11061923	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11061924	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11061925	0.87[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11061927	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11061937	0.91[CEU][hapmap];0.93[YRI][hapmap];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11061940	0.85[AMR][1000 genomes]
rs11061956	0.81[ASN][1000 genomes]
rs11061957	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11061962	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11061968	0.88[AMR][1000 genomes]
rs11061974	0.87[CEU][hapmap];0.87[AMR][1000 genomes]
rs1136213	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11832817	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12231894	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12342	0.84[AMR][1000 genomes]
rs12582624	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12810020	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12812707	0.88[AMR][1000 genomes]
rs12813694	0.87[CEU][hapmap];0.88[AMR][1000 genomes]
rs12828908	0.88[AMR][1000 genomes]
rs12831353	0.88[AMR][1000 genomes]
rs2058034	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2058035	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2240613	0.86[AMR][1000 genomes]
rs2286385	0.86[AMR][1000 genomes]
rs2370055	0.88[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34375871	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3809266	0.86[AMR][1000 genomes]
rs4766413	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6489320	0.83[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs6489323	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6489324	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66590925	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7132033	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7297509	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7313760	0.88[AMR][1000 genomes]
rs7975600	0.94[YRI][hapmap]
rs7975826	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7978818	0.84[CEU][hapmap];0.85[AMR][1000 genomes]
rs929434	0.83[CEU][hapmap];0.88[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	nsv1045312	chr12:1805856-1843202	Enhancers ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:1801600-1823400	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr12:1801600-1827800	Weak transcription	Rectal Smooth Muscle	rectum
3	chr12:1801800-1823800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr12:1801800-1828200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr12:1801800-1830800	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr12:1802200-1822800	Weak transcription	Thymus	Thymus
7	chr12:1802400-1822800	Weak transcription	Fetal Thymus	thymus
8	chr12:1802400-1823000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr12:1802400-1824600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr12:1802400-1841200	Weak transcription	HMEC	breast
11	chr12:1806000-1840000	Weak transcription	Spleen	Spleen
12	chr12:1806200-1823400	Weak transcription	Dnd41	blood
13	chr12:1806200-1844400	Weak transcription	NHEK	skin
14	chr12:1807200-1847400	Weak transcription	Fetal Stomach	stomach
15	chr12:1807400-1819200	Weak transcription	Primary T cells from cord blood	blood
16	chr12:1807400-1822000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr12:1807400-1823400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr12:1807600-1821600	Weak transcription	Ovary	ovary
19	chr12:1807800-1817400	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr12:1808200-1820400	Weak transcription	Fetal Lung	lung
21	chr12:1808200-1820400	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr12:1808400-1830800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr12:1810600-1819800	Weak transcription	Fetal Intestine Small	intestine
24	chr12:1812600-1819400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr12:1813200-1819400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr12:1813200-1823400	Weak transcription	Left Ventricle	heart
27	chr12:1813400-1819200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr12:1813800-1817800	Enhancers	Brain Substantia Nigra	brain
29	chr12:1814400-1825400	Weak transcription	Colon Smooth Muscle	Colon
30	chr12:1814800-1818400	Enhancers	Brain Hippocampus Middle	brain
31	chr12:1815200-1823800	Weak transcription	HSMM	muscle
32	chr12:1815200-1827800	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr12:1815600-1817600	Enhancers	Skeletal Muscle Female	skeletal muscle
34	chr12:1816000-1819000	Weak transcription	Brain Angular Gyrus	brain
35	chr12:1816000-1821600	Weak transcription	Brain Cingulate Gyrus	brain
36	chr12:1816200-1819200	Weak transcription	Psoas Muscle	Psoas
37	chr12:1816200-1819200	Weak transcription	Right Atrium	heart
38	chr12:1816200-1819400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr12:1816200-1820000	Weak transcription	Pancreas	Pancrea
40	chr12:1816200-1820400	Weak transcription	Duodenum Mucosa	Duodenum
41	chr12:1816200-1820400	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr12:1816200-1821800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr12:1816200-1822000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr12:1816200-1822000	Weak transcription	Gastric	stomach
45	chr12:1816200-1822200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr12:1816200-1825200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr12:1816200-1825400	Weak transcription	Osteobl	bone
48	chr12:1816200-1836400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr12:1816200-1849400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr12:1816200-1857800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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