Variant report

Variant	rs12579507
Chromosome Location	chr12:1810374-1810375
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:1810359-1810374	MCF-7	breast:	n/a	n/a
2	SETDB1	chr12:1809899-1810703	U2OS	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:1797812..1801808-chr12:1810068..1813967,7	MCF-7	breast:
2	chr12:1769759..1773174-chr12:1808605..1811319,4	K562	blood:
3	chr12:1807973..1810676-chr12:1846571..1848723,2	K562	blood:
4	chr12:1807832..1811641-chr12:1812567..1815374,5	K562	blood:

Variant related genes	Relation type
ENSG00000271500	TF binding region
ENSG00000006831	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10848566	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11061918	0.97[ASN][1000 genomes]
rs11061921	0.80[ASN][1000 genomes]
rs11061927	0.83[ASN][1000 genomes]
rs11061935	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11061946	0.90[ASN][1000 genomes]
rs11061952	0.90[ASN][1000 genomes]
rs11061956	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11061967	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11061973	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1136213	0.80[ASN][1000 genomes]
rs11833054	0.90[ASN][1000 genomes]
rs12230440	0.86[AFR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12581815	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12821401	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16928704	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2058033	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2058034	0.82[ASN][1000 genomes]
rs35396561	0.80[AFR][1000 genomes]
rs6489323	0.82[ASN][1000 genomes]
rs7132033	0.83[ASN][1000 genomes]
rs71454839	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73040715	0.92[ASN][1000 genomes]
rs73040736	0.90[ASN][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	chr12:1801800-1811400	Weak transcription	NH-A	brain
8	chr12:1801800-1813400	Weak transcription	A549	lung
9	chr12:1801800-1823800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr12:1801800-1828200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr12:1801800-1830800	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr12:1802200-1815000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr12:1802200-1815000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr12:1802200-1815000	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr12:1802200-1815400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr12:1802200-1815800	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr12:1802200-1822800	Weak transcription	Thymus	Thymus
18	chr12:1802400-1811800	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr12:1802400-1815000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr12:1802400-1822800	Weak transcription	Fetal Thymus	thymus
21	chr12:1802400-1823000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr12:1802400-1824600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr12:1802400-1841200	Weak transcription	HMEC	breast
24	chr12:1803000-1813400	Weak transcription	Primary B cells from cord blood	blood
25	chr12:1803200-1815800	Weak transcription	Primary B cells from peripheral blood	blood
26	chr12:1803800-1812400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr12:1804400-1816000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr12:1805400-1813400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr12:1805400-1814800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr12:1806000-1815200	Weak transcription	Primary monocytes fromperipheralblood	blood
31	chr12:1806000-1815800	Weak transcription	Lung	lung
32	chr12:1806000-1840000	Weak transcription	Spleen	Spleen
33	chr12:1806200-1823400	Weak transcription	Dnd41	blood
34	chr12:1806200-1844400	Weak transcription	NHEK	skin
35	chr12:1806400-1815000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr12:1806600-1815800	Weak transcription	NHDF-Ad	bronchial
37	chr12:1806800-1811200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr12:1806800-1813800	Weak transcription	Primary hematopoietic stem cells	blood
39	chr12:1806800-1815000	Weak transcription	Brain Angular Gyrus	brain
40	chr12:1807000-1814000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr12:1807200-1811400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr12:1807200-1847400	Weak transcription	Fetal Stomach	stomach
43	chr12:1807400-1812000	Weak transcription	Colon Smooth Muscle	Colon
44	chr12:1807400-1819200	Weak transcription	Primary T cells from cord blood	blood
45	chr12:1807400-1822000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr12:1807400-1823400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr12:1807600-1811000	Weak transcription	Psoas Muscle	Psoas
48	chr12:1807600-1812400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr12:1807600-1812600	Weak transcription	Left Ventricle	heart
50	chr12:1807600-1813600	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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