Variant report

Variant	rs12046600
Chromosome Location	chr1:56104582-56104583
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11206646	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12029835	0.92[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.86[ASN][1000 genomes]
rs12035892	0.84[CHB][hapmap]
rs12047589	0.84[CHB][hapmap]
rs12403776	0.91[CHB][hapmap]
rs1392138	1.00[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1392139	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1499674	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1499675	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17112559	0.92[CHB][hapmap];0.92[ASN][1000 genomes]
rs17112560	0.81[ASW][hapmap];0.92[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];0.97[MKK][hapmap];0.90[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs17112610	0.84[CHB][hapmap];0.80[ASN][1000 genomes]
rs17112615	0.84[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.80[ASN][1000 genomes]
rs17112658	0.84[CHB][hapmap]
rs1828802	0.82[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.95[MKK][hapmap];0.92[ASN][1000 genomes]
rs1976362	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3862236	0.84[CHB][hapmap];1.00[GIH][hapmap]
rs3889741	0.84[CHB][hapmap]
rs3914412	0.84[CHB][hapmap]
rs4317850	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6672047	0.84[CHB][hapmap];1.00[GIH][hapmap]
rs6689891	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6693323	1.00[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74072496	0.92[ASN][1000 genomes]
rs7513796	0.84[CHB][hapmap]
rs7551229	0.84[CHB][hapmap]
rs769973	0.92[CHB][hapmap];0.92[ASN][1000 genomes]

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	nsv461617	chr1:56055190-56123510	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
2	nsv546303	chr1:56055190-56123510	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
3	nsv1014866	chr1:56059054-56129092	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	nsv526148	chr1:56101597-56146450	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12046600	GSTM1	trans	lymphoblastoid	seeQTL

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:56098800-56105800	Weak transcription	Fetal Stomach	stomach
2	chr1:56099000-56105200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr1:56099000-56106600	Weak transcription	Ovary	ovary
4	chr1:56099200-56105800	Weak transcription	Fetal Kidney	kidney
5	chr1:56100600-56106600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr1:56100800-56104800	Weak transcription	Hela-S3	cervix
7	chr1:56100800-56106600	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr1:56101200-56105000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr1:56101200-56105800	Weak transcription	Psoas Muscle	Psoas
10	chr1:56101800-56106600	Weak transcription	Fetal Lung	lung
11	chr1:56102200-56106000	Weak transcription	NHLF	lung
12	chr1:56102400-56105200	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr1:56102400-56106000	Weak transcription	Aorta	Aorta
14	chr1:56102400-56106400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr1:56102600-56105800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr1:56102800-56105000	Weak transcription	Osteobl	bone
17	chr1:56103000-56106400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr1:56103400-56106000	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr1:56103400-56106400	Weak transcription	NHDF-Ad	bronchial
20	chr1:56103400-56107000	Weak transcription	Gastric	stomach
21	chr1:56103800-56104800	Enhancers	Fetal Heart	heart
22	chr1:56104000-56105600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr1:56104200-56106400	Enhancers	Breast Myoepithelial Primary Cells	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links