Variant report

Variant	rs11061927
Chromosome Location	chr12:1805467-1805468
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:1801036..1802914-chr12:1804421..1806179,3	MCF-7	breast:
2	chr12:1769488..1776078-chr12:1798561..1806450,20	K562	blood:
3	chr12:1805184..1807328-chr12:1869608..1872383,2	K562	blood:
4	chr12:1770854..1772922-chr12:1803554..1806296,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CACNA2D4-2	chr12:1804996-1805554	NONHSAT025413

Variant related genes	Relation type
ENSG00000266043	Chromatin interaction
ENSG00000006831	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1029629	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10773982	0.82[CEU][hapmap]
rs10773986	0.84[CEU][hapmap];0.88[YRI][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10848551	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10848552	0.97[ASN][1000 genomes]
rs10848553	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10848558	0.82[AMR][1000 genomes]
rs10848566	0.81[ASN][1000 genomes]
rs10848569	0.85[AMR][1000 genomes]
rs11061918	0.81[JPT][hapmap]
rs11061919	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11061920	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11061921	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11061923	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11061924	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11061925	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11061935	0.80[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs11061937	0.86[CEU][hapmap];0.93[YRI][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11061940	0.82[AMR][1000 genomes]
rs11061946	0.80[CHB][hapmap]
rs11061952	0.80[CHB][hapmap]
rs11061956	0.81[ASN][1000 genomes]
rs11061957	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11061962	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11061967	0.80[CHB][hapmap]
rs11061968	0.85[AMR][1000 genomes]
rs11061974	0.82[CEU][hapmap];0.84[AMR][1000 genomes]
rs1136213	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11832817	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]
rs12230440	0.80[CHB][hapmap];0.85[JPT][hapmap]
rs12230579	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]
rs12231894	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12342	0.81[AMR][1000 genomes]
rs12579507	0.83[ASN][1000 genomes]
rs12582624	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12810020	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12812707	0.85[AMR][1000 genomes]
rs12813694	0.82[CEU][hapmap];0.85[AMR][1000 genomes]
rs12821401	0.80[CHB][hapmap]
rs12828908	0.85[AMR][1000 genomes]
rs12831353	0.85[AMR][1000 genomes]
rs2058033	0.80[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs2058034	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2058035	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2240613	0.83[AMR][1000 genomes]
rs2286385	0.83[AMR][1000 genomes]
rs2370055	0.83[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34375871	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3809266	0.83[AMR][1000 genomes]
rs4766413	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6489320	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6489323	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6489324	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66590925	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7132033	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];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7297509	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7313760	0.85[AMR][1000 genomes]
rs7975600	0.94[YRI][hapmap]
rs7975826	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7978818	0.82[AMR][1000 genomes]
rs929434	0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:1801000-1805600	Weak transcription	Pancreas	Pancrea
2	chr12:1801000-1815800	Weak transcription	Esophagus	oesophagus
3	chr12:1801000-1815800	Weak transcription	Gastric	stomach
4	chr12:1801200-1807200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr12:1801400-1806400	Weak transcription	Fetal Lung	lung
6	chr12:1801400-1806600	Weak transcription	Aorta	Aorta
7	chr12:1801600-1806000	Weak transcription	Colon Smooth Muscle	Colon
8	chr12:1801600-1806600	Weak transcription	Fetal Brain Male	brain
9	chr12:1801600-1807600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr12:1801600-1814200	Weak transcription	HSMM	muscle
11	chr12:1801600-1815200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr12:1801600-1823400	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr12:1801600-1827800	Weak transcription	Rectal Smooth Muscle	rectum
14	chr12:1801800-1805600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr12:1801800-1805800	Weak transcription	NHLF	lung
16	chr12:1801800-1806000	Weak transcription	Primary T cells from cord blood	blood
17	chr12:1801800-1807800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr12:1801800-1808200	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr12:1801800-1811400	Weak transcription	NH-A	brain
20	chr12:1801800-1813400	Weak transcription	A549	lung
21	chr12:1801800-1823800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr12:1801800-1828200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr12:1801800-1830800	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr12:1802200-1805600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr12:1802200-1805600	Weak transcription	Lung	lung
26	chr12:1802200-1805600	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr12:1802200-1805800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr12:1802200-1805800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr12:1802200-1806000	Weak transcription	Stomach Smooth Muscle	stomach
30	chr12:1802200-1806400	Weak transcription	Right Ventricle	heart
31	chr12:1802200-1806600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr12:1802200-1806600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr12:1802200-1806600	Weak transcription	Fetal Brain Female	brain
34	chr12:1802200-1807800	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr12:1802200-1815000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr12:1802200-1815000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr12:1802200-1815000	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr12:1802200-1815400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr12:1802200-1815800	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr12:1802200-1822800	Weak transcription	Thymus	Thymus
41	chr12:1802400-1805600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr12:1802400-1805600	Weak transcription	Left Ventricle	heart
43	chr12:1802400-1806000	Weak transcription	Fetal Stomach	stomach
44	chr12:1802400-1808800	Weak transcription	HUVEC	blood vessel
45	chr12:1802400-1811800	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr12:1802400-1815000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr12:1802400-1822800	Weak transcription	Fetal Thymus	thymus
48	chr12:1802400-1823000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr12:1802400-1824600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr12:1802400-1841200	Weak transcription	HMEC	breast

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