Variant report

Variant	rs12492309
Chromosome Location	chr3:110810450-110810451
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10433385	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10433386	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10934073	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10934074	0.87[AMR][1000 genomes]
rs12108091	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12487779	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12488066	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1351050	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1381837	0.90[CHB][hapmap]
rs1477841	0.83[JPT][hapmap]
rs1477843	0.83[JPT][hapmap]
rs1477847	0.82[JPT][hapmap]
rs2126713	0.83[JPT][hapmap]
rs2399373	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs4682229	0.83[JPT][hapmap]
rs4682230	0.83[JPT][hapmap]
rs4682231	0.83[JPT][hapmap]
rs4682234	0.83[JPT][hapmap]
rs6437948	0.83[JPT][hapmap]
rs6765133	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72622317	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72935996	0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7612667	0.83[JPT][hapmap]
rs7653595	0.83[JPT][hapmap]
rs9821335	0.83[JPT][hapmap]
rs9828899	0.83[JPT][hapmap]
rs9866028	0.83[JPT][hapmap]
rs9876350	0.83[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003106	chr3:110264476-111105943	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv460821	chr3:110637471-111501097	Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv591275	chr3:110637471-111501097	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	esv1850918	chr3:110685181-110889974	Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:110794400-110813600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr3:110799800-110820600	Weak transcription	A549	lung
3	chr3:110800200-110812400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr3:110800200-110817200	Weak transcription	Gastric	stomach
5	chr3:110802000-110822600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr3:110804000-110817200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr3:110804200-110814200	Weak transcription	Fetal Intestine Large	intestine
8	chr3:110804800-110811400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr3:110805000-110833600	Weak transcription	NHDF-Ad	bronchial
10	chr3:110805600-110810800	Weak transcription	Colon Smooth Muscle	Colon
11	chr3:110807000-110813200	Weak transcription	Fetal Intestine Small	intestine
12	chr3:110807000-110815400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr3:110807200-110811600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr3:110807200-110813200	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr3:110807200-110813400	Weak transcription	Ovary	ovary
16	chr3:110807200-110814600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr3:110807200-110815400	Weak transcription	Psoas Muscle	Psoas
18	chr3:110807200-110822600	Weak transcription	Fetal Lung	lung
19	chr3:110807400-110813200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr3:110807400-110815200	Weak transcription	Fetal Heart	heart
21	chr3:110807600-110813400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr3:110807800-110811200	Enhancers	iPS-18 Cell Line	embryonic stem cell
23	chr3:110807800-110812600	Weak transcription	Dnd41	blood
24	chr3:110808600-110817200	Weak transcription	Small Intestine	intestine
25	chr3:110808800-110813200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr3:110808800-110813600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr3:110809400-110813000	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr3:110809400-110813200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr3:110810400-110816400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links