Variant report

Variant	rs1109858
Chromosome Location	chr3:133089075-133089076
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1114630	0.82[JPT][hapmap]
rs1197282	1.00[ASW][hapmap];0.83[CEU][hapmap];1.00[MEX][hapmap];0.83[AMR][1000 genomes]
rs1197283	0.83[CEU][hapmap];0.83[AMR][1000 genomes]
rs1197288	0.82[JPT][hapmap]
rs1197289	0.82[JPT][hapmap]
rs1197293	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs1197296	0.82[JPT][hapmap]
rs1197298	0.82[JPT][hapmap]
rs1197299	0.82[JPT][hapmap]
rs1197302	0.82[JPT][hapmap]
rs1197304	0.82[JPT][hapmap]
rs1197305	0.82[JPT][hapmap]
rs1197306	0.82[JPT][hapmap]
rs1197308	1.00[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1197309	0.82[JPT][hapmap]
rs1197311	1.00[YRI][hapmap]
rs1197313	0.82[JPT][hapmap]
rs1197314	0.82[JPT][hapmap]
rs1201671	0.82[JPT][hapmap]
rs1201674	0.89[AMR][1000 genomes]
rs12495802	0.83[CEU][hapmap];0.83[AMR][1000 genomes]
rs12630350	0.84[MEX][hapmap]
rs12633430	0.86[AMR][1000 genomes]
rs1513366	0.83[CEU][hapmap];0.83[AMR][1000 genomes]
rs1567788	1.00[ASW][hapmap];0.80[CEU][hapmap];0.80[CHB][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs1619552	0.82[JPT][hapmap]
rs1619622	0.82[JPT][hapmap]
rs16840105	0.83[CEU][hapmap];0.83[MEX][hapmap];0.83[AMR][1000 genomes]
rs16840179	1.00[ASW][hapmap];0.83[CEU][hapmap];1.00[MEX][hapmap];0.86[AMR][1000 genomes]
rs1708355	0.83[AMR][1000 genomes]
rs1708357	0.81[CEU][hapmap];0.89[AMR][1000 genomes]
rs1708367	0.91[CEU][hapmap];0.83[AMR][1000 genomes]
rs1708368	0.83[CEU][hapmap];0.94[MEX][hapmap];0.83[AMR][1000 genomes]
rs1708370	0.83[AMR][1000 genomes]
rs1708377	0.82[JPT][hapmap]
rs1708386	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1795097	0.83[AMR][1000 genomes]
rs1795101	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1795107	0.82[JPT][hapmap]
rs2060639	0.83[CEU][hapmap];0.94[MEX][hapmap];0.83[AMR][1000 genomes]
rs2670179	0.82[JPT][hapmap]
rs2670182	0.83[AMR][1000 genomes]
rs2699882	0.82[JPT][hapmap]
rs4854576	0.83[CEU][hapmap];0.89[MEX][hapmap]
rs4854582	0.83[CEU][hapmap];0.89[AMR][1000 genomes]
rs4854704	0.83[CEU][hapmap]
rs4854708	1.00[ASW][hapmap];0.83[CEU][hapmap];1.00[MEX][hapmap];0.83[AMR][1000 genomes]
rs553211	1.00[YRI][hapmap]
rs55719274	0.83[AMR][1000 genomes]
rs56269716	0.83[AMR][1000 genomes]
rs59171035	0.83[AMR][1000 genomes]
rs59885161	0.83[AMR][1000 genomes]
rs869751	0.82[JPT][hapmap]
rs938229	0.82[JPT][hapmap]
rs938238	0.83[CEU][hapmap];0.94[MEX][hapmap];0.86[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877503	chr3:133035774-133104631	Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:133080800-133098600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr3:133081800-133090000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr3:133083200-133099200	Weak transcription	Lung	lung
4	chr3:133085800-133091600	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr3:133086200-133090200	Enhancers	Fetal Brain Female	brain
6	chr3:133086200-133090800	Enhancers	Brain Cingulate Gyrus	brain
7	chr3:133086400-133090400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr3:133086800-133089800	Enhancers	Brain Germinal Matrix	brain
9	chr3:133088000-133089200	Weak transcription	Brain Hippocampus Middle	brain
10	chr3:133088000-133091000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr3:133088000-133093800	Weak transcription	HSMMtube	muscle
12	chr3:133088200-133089200	Weak transcription	Fetal Brain Male	brain
13	chr3:133088600-133089800	Enhancers	Brain Inferior Temporal Lobe	brain
14	chr3:133088600-133090400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr3:133088800-133089600	Enhancers	Brain Substantia Nigra	brain
16	chr3:133088800-133090000	Enhancers	Brain Angular Gyrus	brain
17	chr3:133089000-133089200	Enhancers	Fetal Lung	lung
18	chr3:133089000-133089600	Enhancers	Brain Anterior Caudate	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links