Variant report

Variant	rs6489323
Chromosome Location	chr12:1813758-1813759
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:1797812..1801808-chr12:1810068..1813967,7	MCF-7	breast:
2	chr12:1807832..1811641-chr12:1812567..1815374,5	K562	blood:
3	chr12:1797706..1801661-chr12:1812450..1816186,4	MCF-7	breast:
4	chr12:1812993..1815717-chr12:1847079..1848811,2	K562	blood:

Variant related genes	Relation type
ENSG00000006831	Chromatin interaction

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

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

rs_ID	r²[population]
rs1029629	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10773986	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10848551	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10848552	0.96[ASN][1000 genomes]
rs10848553	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10848558	0.83[AMR][1000 genomes]
rs10848566	0.80[ASN][1000 genomes]
rs10848569	0.86[AMR][1000 genomes]
rs11061919	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11061920	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11061921	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11061923	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11061924	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11061925	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11061927	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11061935	0.83[ASN][1000 genomes]
rs11061937	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11061940	0.83[AMR][1000 genomes]
rs11061956	0.80[ASN][1000 genomes]
rs11061957	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11061962	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11061968	0.86[AMR][1000 genomes]
rs11061974	0.85[AMR][1000 genomes]
rs1136213	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11832817	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12230579	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12231894	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12342	0.82[AMR][1000 genomes]
rs12579507	0.82[ASN][1000 genomes]
rs12582624	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12810020	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12812707	0.86[AMR][1000 genomes]
rs12813694	0.86[AMR][1000 genomes]
rs12828908	0.86[AMR][1000 genomes]
rs12831353	0.86[AMR][1000 genomes]
rs2058033	0.83[ASN][1000 genomes]
rs2058034	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2058035	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2240613	0.84[AMR][1000 genomes]
rs2286385	0.84[AMR][1000 genomes]
rs2370055	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34375871	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3809266	0.84[AMR][1000 genomes]
rs4766413	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6489320	0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs6489324	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs66590925	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7132033	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7297509	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7313760	0.86[AMR][1000 genomes]
rs7975826	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7978818	0.83[AMR][1000 genomes]
rs929434	0.86[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:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:1801000-1815800	Weak transcription	Esophagus	oesophagus
2	chr12:1801000-1815800	Weak transcription	Gastric	stomach
3	chr12:1801600-1814200	Weak transcription	HSMM	muscle
4	chr12:1801600-1815200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr12:1801600-1823400	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr12:1801600-1827800	Weak transcription	Rectal Smooth Muscle	rectum
7	chr12:1801800-1823800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr12:1801800-1828200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr12:1801800-1830800	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr12:1802200-1815000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr12:1802200-1815000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr12:1802200-1815000	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr12:1802200-1815400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr12:1802200-1815800	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr12:1802200-1822800	Weak transcription	Thymus	Thymus
16	chr12:1802400-1815000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr12:1802400-1822800	Weak transcription	Fetal Thymus	thymus
18	chr12:1802400-1823000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr12:1802400-1824600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr12:1802400-1841200	Weak transcription	HMEC	breast
21	chr12:1803200-1815800	Weak transcription	Primary B cells from peripheral blood	blood
22	chr12:1804400-1816000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr12:1805400-1814800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr12:1806000-1815200	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr12:1806000-1815800	Weak transcription	Lung	lung
26	chr12:1806000-1840000	Weak transcription	Spleen	Spleen
27	chr12:1806200-1823400	Weak transcription	Dnd41	blood
28	chr12:1806200-1844400	Weak transcription	NHEK	skin
29	chr12:1806400-1815000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr12:1806600-1815800	Weak transcription	NHDF-Ad	bronchial
31	chr12:1806800-1813800	Weak transcription	Primary hematopoietic stem cells	blood
32	chr12:1806800-1815000	Weak transcription	Brain Angular Gyrus	brain
33	chr12:1807000-1814000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr12:1807200-1847400	Weak transcription	Fetal Stomach	stomach
35	chr12:1807400-1819200	Weak transcription	Primary T cells from cord blood	blood
36	chr12:1807400-1822000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr12:1807400-1823400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr12:1807600-1815200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr12:1807600-1815800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr12:1807600-1815800	Weak transcription	Pancreas	Pancrea
41	chr12:1807600-1815800	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr12:1807600-1821600	Weak transcription	Ovary	ovary
43	chr12:1807800-1817400	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr12:1808200-1814200	Weak transcription	Brain Cingulate Gyrus	brain
45	chr12:1808200-1815000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr12:1808200-1815200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr12:1808200-1815200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr12:1808200-1820400	Weak transcription	Fetal Lung	lung
49	chr12:1808200-1820400	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr12:1808400-1815000	Weak transcription	Rectal Mucosa Donor 29	rectum

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