Variant report

Variant	rs12820515
Chromosome Location	chr12:29308527-29308528
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:29300317..29304551-chr12:29306298..29309570,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000064763	Chromatin interaction
ENSG00000257258	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10843325	1.00[AMR][1000 genomes]
rs12811417	1.00[EUR][1000 genomes]
rs12815733	1.00[EUR][1000 genomes]
rs12816534	1.00[EUR][1000 genomes]
rs12817351	1.00[EUR][1000 genomes]
rs12819686	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12826306	1.00[EUR][1000 genomes]
rs12831837	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12832977	1.00[EUR][1000 genomes]
rs34064202	1.00[EUR][1000 genomes]
rs34158620	1.00[EUR][1000 genomes]
rs34170651	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34237455	1.00[EUR][1000 genomes]
rs34270636	1.00[EUR][1000 genomes]
rs34339523	1.00[EUR][1000 genomes]
rs34391841	1.00[EUR][1000 genomes]
rs34492685	1.00[EUR][1000 genomes]
rs34526565	1.00[EUR][1000 genomes]
rs34572599	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34601700	1.00[EUR][1000 genomes]
rs34624113	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34685180	1.00[EUR][1000 genomes]
rs34690032	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34825983	1.00[EUR][1000 genomes]
rs34879577	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34941964	1.00[EUR][1000 genomes]
rs34990495	1.00[EUR][1000 genomes]
rs35002558	1.00[EUR][1000 genomes]
rs35039649	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35042869	1.00[EUR][1000 genomes]
rs35054952	1.00[EUR][1000 genomes]
rs35071007	1.00[EUR][1000 genomes]
rs35100017	1.00[EUR][1000 genomes]
rs35121122	1.00[EUR][1000 genomes]
rs35195316	1.00[EUR][1000 genomes]
rs35199330	1.00[EUR][1000 genomes]
rs35426167	1.00[EUR][1000 genomes]
rs35447364	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35708989	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35736217	1.00[EUR][1000 genomes]
rs35763553	1.00[EUR][1000 genomes]
rs35773649	1.00[EUR][1000 genomes]
rs35776525	1.00[EUR][1000 genomes]
rs35779561	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs35861754	1.00[EUR][1000 genomes]
rs55710291	1.00[AMR][1000 genomes]
rs55880276	1.00[AMR][1000 genomes]
rs56269416	1.00[AMR][1000 genomes]
rs57106561	1.00[AMR][1000 genomes]
rs59663308	1.00[AMR][1000 genomes]
rs60656521	1.00[AMR][1000 genomes]
rs6487777	1.00[AMR][1000 genomes]
rs71453725	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs71453726	1.00[EUR][1000 genomes]
rs71453728	1.00[EUR][1000 genomes]
rs71453729	1.00[EUR][1000 genomes]
rs7315584	1.00[EUR][1000 genomes]
rs74076456	1.00[AMR][1000 genomes]
rs74076489	1.00[AMR][1000 genomes]
rs74076501	1.00[AMR][1000 genomes]
rs74077035	1.00[AMR][1000 genomes]
rs7955386	1.00[EUR][1000 genomes]
rs7972299	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532233	chr12:29009388-29496179	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv995123	chr12:29095272-29571558	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv1053641	chr12:29268813-29854413	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer 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	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29303200-29309800	Weak transcription	NHDF-Ad	bronchial
2	chr12:29303400-29309000	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr12:29303400-29309800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr12:29303400-29311400	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr12:29303400-29312200	Weak transcription	Spleen	Spleen
6	chr12:29303400-29316600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr12:29303400-29317000	Weak transcription	Colonic Mucosa	Colon
8	chr12:29303400-29317800	Weak transcription	Fetal Kidney	kidney
9	chr12:29303600-29308800	Enhancers	Dnd41	blood
10	chr12:29303600-29313400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr12:29303800-29310200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr12:29304000-29312600	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr12:29304400-29308800	Enhancers	Primary B cells from cord blood	blood
14	chr12:29306000-29312400	Weak transcription	Duodenum Mucosa	Duodenum
15	chr12:29306400-29310400	Weak transcription	Right Atrium	heart
16	chr12:29306400-29313000	Weak transcription	Rectal Smooth Muscle	rectum
17	chr12:29306400-29313200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr12:29306600-29308600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr12:29306600-29310400	Enhancers	Primary neutrophils fromperipheralblood	blood
20	chr12:29306600-29310600	Weak transcription	Adipose Nuclei	Adipose
21	chr12:29306600-29312600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr12:29306600-29312600	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr12:29306600-29313000	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr12:29306600-29324600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr12:29306800-29310400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr12:29306800-29313200	Weak transcription	Fetal Thymus	thymus
27	chr12:29306800-29324400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr12:29307400-29308600	Enhancers	Fetal Intestine Large	intestine
29	chr12:29307600-29308600	Enhancers	Primary hematopoietic stem cells	blood
30	chr12:29307600-29308600	Enhancers	Placenta	Placenta
31	chr12:29308200-29308600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr12:29308200-29308600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
33	chr12:29308400-29308600	Enhancers	Small Intestine	intestine
34	chr12:29308400-29308600	Enhancers	GM12878-XiMat	blood
35	chr12:29308400-29309000	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr12:29308400-29309200	Weak transcription	HUVEC	blood vessel
37	chr12:29308400-29309400	Weak transcription	Brain Hippocampus Middle	brain
38	chr12:29308400-29309600	Weak transcription	Monocytes-CD14+_RO01746	blood
39	chr12:29308400-29309600	Weak transcription	NH-A	brain
40	chr12:29308400-29310200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr12:29308400-29310200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr12:29308400-29310200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr12:29308400-29312600	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr12:29308400-29312600	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr12:29308400-29312600	Weak transcription	K562	blood
46	chr12:29308400-29313200	Weak transcription	Brain Anterior Caudate	brain
47	chr12:29308400-29317000	Weak transcription	Fetal Intestine Small	intestine
48	chr12:29308400-29324000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr12:29308400-29324400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links