Variant report

Variant	rs1908689
Chromosome Location	chr12:29309231-29309232
allele	A/C
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: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10771487	0.89[CEU][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10771488	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10771490	0.95[CEU][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10843339	0.94[CEU][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11050098	0.83[YRI][hapmap];0.82[AFR][1000 genomes]
rs12372303	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12372311	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12372469	0.95[CEU][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1496212	0.94[CEU][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1561131	0.95[CEU][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1865768	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3858548	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4930855	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4931160	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4931161	0.94[CEU][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6487778	0.83[YRI][hapmap]
rs6487779	0.95[CEU][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6487781	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6487784	0.90[EUR][1000 genomes]
rs6487785	0.94[CEU][hapmap];0.91[EUR][1000 genomes]
rs7136626	0.95[CEU][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7297280	0.95[CEU][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7961901	0.94[CEU][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7962453	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7970668	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7971179	0.94[CEU][hapmap];0.81[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][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:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29303200-29309800	Weak transcription	NHDF-Ad	bronchial
2	chr12:29303400-29309800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr12:29303400-29311400	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr12:29303400-29312200	Weak transcription	Spleen	Spleen
5	chr12:29303400-29316600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr12:29303400-29317000	Weak transcription	Colonic Mucosa	Colon
7	chr12:29303400-29317800	Weak transcription	Fetal Kidney	kidney
8	chr12:29303600-29313400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr12:29303800-29310200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr12:29304000-29312600	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr12:29306000-29312400	Weak transcription	Duodenum Mucosa	Duodenum
12	chr12:29306400-29310400	Weak transcription	Right Atrium	heart
13	chr12:29306400-29313000	Weak transcription	Rectal Smooth Muscle	rectum
14	chr12:29306400-29313200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr12:29306600-29310400	Enhancers	Primary neutrophils fromperipheralblood	blood
16	chr12:29306600-29310600	Weak transcription	Adipose Nuclei	Adipose
17	chr12:29306600-29312600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr12:29306600-29312600	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr12:29306600-29313000	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr12:29306600-29324600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr12:29306800-29310400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr12:29306800-29313200	Weak transcription	Fetal Thymus	thymus
23	chr12:29306800-29324400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr12:29308400-29309400	Weak transcription	Brain Hippocampus Middle	brain
25	chr12:29308400-29309600	Weak transcription	Monocytes-CD14+_RO01746	blood
26	chr12:29308400-29309600	Weak transcription	NH-A	brain
27	chr12:29308400-29310200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr12:29308400-29310200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr12:29308400-29310200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr12:29308400-29312600	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr12:29308400-29312600	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr12:29308400-29312600	Weak transcription	K562	blood
33	chr12:29308400-29313200	Weak transcription	Brain Anterior Caudate	brain
34	chr12:29308400-29317000	Weak transcription	Fetal Intestine Small	intestine
35	chr12:29308400-29324000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr12:29308400-29324400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr12:29308600-29310200	Enhancers	Primary hematopoietic stem cells short term culture	blood
38	chr12:29308600-29310400	Weak transcription	Placenta	Placenta
39	chr12:29308600-29311200	Weak transcription	GM12878-XiMat	blood
40	chr12:29308600-29312600	Weak transcription	Small Intestine	intestine
41	chr12:29308800-29309800	Weak transcription	Primary B cells from cord blood	blood
42	chr12:29308800-29317200	Weak transcription	Dnd41	blood
43	chr12:29309000-29309400	Weak transcription	Primary monocytes fromperipheralblood	blood
44	chr12:29309000-29310400	Enhancers	Primary hematopoietic stem cells	blood
45	chr12:29309200-29312600	Enhancers	HUVEC	blood vessel

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links