Variant report

Variant	rs12229790
Chromosome Location	chr12:64259984-64259985
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:64259856..64261721-chr12:64265461..64267447,2	MCF-7	breast:
2	chr12:64257945..64259859-chr12:64259892..64262492,3	MCF-7	breast:
3	chr12:64254678..64258025-chr12:64259314..64262432,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000242087	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs11175184	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11175185	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11175188	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11175189	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11175197	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11833808	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11835034	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12228199	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17099866	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2335884	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35143986	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4072758	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55642517	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55655348	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55760535	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55907605	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55930806	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56028204	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56080061	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56264182	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58424013	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59063572	0.82[EUR][1000 genomes]
rs60031756	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6581509	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6581510	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66856673	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67401817	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67684483	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs67830727	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67880496	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67892056	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67993208	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs68188132	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7136130	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7294327	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7301437	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7302672	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7304340	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7305893	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7307108	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7308850	0.83[ASN][1000 genomes]
rs7310327	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7310329	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7310575	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7311611	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73313479	0.84[AFR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73315321	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73315365	0.98[ASN][1000 genomes]
rs7953208	0.80[AMR][1000 genomes];0.97[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	nsv1046836	chr12:63392391-64377169	Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
2	esv2751110	chr12:63939733-64274680	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv832442	chr12:64228071-64442771	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	esv1810729	chr12:64234926-64268005	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	n/a
5	esv1833454	chr12:64237504-64264837	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	n/a
6	esv1803717	chr12:64250221-64261249	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:64241000-64261200	Weak transcription	Fetal Muscle Trunk	muscle
2	chr12:64241000-64268800	Weak transcription	Lung	lung
3	chr12:64241000-64278800	Weak transcription	Fetal Stomach	stomach
4	chr12:64243400-64263000	Weak transcription	NHEK	skin
5	chr12:64244000-64263600	Weak transcription	Fetal Lung	lung
6	chr12:64246200-64286400	Weak transcription	Fetal Brain Female	brain
7	chr12:64247800-64268200	Weak transcription	Fetal Brain Male	brain
8	chr12:64250200-64287200	Weak transcription	Aorta	Aorta
9	chr12:64256600-64262200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr12:64256600-64263600	Weak transcription	HSMMtube	muscle
11	chr12:64256800-64260200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr12:64256800-64260600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr12:64256800-64262200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr12:64256800-64263200	Weak transcription	Right Atrium	heart
15	chr12:64256800-64271400	Weak transcription	Brain Angular Gyrus	brain
16	chr12:64256800-64276600	Weak transcription	HSMM	muscle
17	chr12:64256800-64282600	Weak transcription	Gastric	stomach
18	chr12:64257000-64262600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr12:64257000-64262800	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr12:64257000-64263600	Weak transcription	NH-A	brain
21	chr12:64257400-64262000	Weak transcription	Left Ventricle	heart
22	chr12:64257400-64263200	Weak transcription	NHDF-Ad	bronchial
23	chr12:64257400-64270600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr12:64257800-64262800	Weak transcription	HMEC	breast
25	chr12:64258000-64262800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr12:64258000-64263000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr12:64258200-64261000	Weak transcription	Rectal Smooth Muscle	rectum
28	chr12:64258200-64262600	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr12:64258200-64262800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr12:64258200-64263200	Weak transcription	NHLF	lung
31	chr12:64258400-64260600	Weak transcription	Stomach Mucosa	stomach
32	chr12:64258400-64262800	Weak transcription	Osteobl	bone
33	chr12:64258400-64263000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr12:64258400-64263400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr12:64258600-64262400	Weak transcription	Hela-S3	cervix
36	chr12:64258600-64263000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr12:64258600-64263000	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr12:64258800-64286200	Weak transcription	Fetal Intestine Small	intestine
39	chr12:64259000-64260200	Enhancers	HUES6 Cell Line	embryonic stem cell
40	chr12:64259000-64263000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr12:64259200-64260200	Enhancers	H9 Cell Line	embryonic stem cell
42	chr12:64259200-64260400	Enhancers	HUES64 Cell Line	embryonic stem cell
43	chr12:64259200-64266800	Weak transcription	Fetal Intestine Large	intestine
44	chr12:64259400-64260000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr12:64259400-64260200	Enhancers	H1 Cell Line	embryonic stem cell
46	chr12:64259400-64260200	Enhancers	HUES48 Cell Line	embryonic stem cell
47	chr12:64259400-64260200	Enhancers	iPS-18 Cell Line	embryonic stem cell
48	chr12:64259400-64260400	Enhancers	iPS-15b Cell Line	embryonic stem cell
49	chr12:64259600-64260800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
50	chr12:64259600-64261200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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