Variant report

Variant	rs2088019
Chromosome Location	chr12:105166229-105166230
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1038968	0.89[EUR][1000 genomes]
rs1316594	0.83[EUR][1000 genomes]
rs1389609	0.80[EUR][1000 genomes]
rs1389610	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1389611	0.91[EUR][1000 genomes]
rs1565815	0.83[EUR][1000 genomes]
rs2004806	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2047124	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2131806	0.81[EUR][1000 genomes]
rs2245927	0.83[EUR][1000 genomes]
rs2245929	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2245931	0.83[EUR][1000 genomes]
rs2453154	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2453155	0.86[EUR][1000 genomes]
rs2453158	0.81[EUR][1000 genomes]
rs2453167	0.83[EUR][1000 genomes]
rs2453168	0.80[EUR][1000 genomes]
rs2463016	0.83[EUR][1000 genomes]
rs2463017	0.83[EUR][1000 genomes]
rs2463020	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2463025	0.83[EUR][1000 genomes]
rs2463429	0.80[EUR][1000 genomes]
rs2463431	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2463432	0.83[EUR][1000 genomes]
rs2463433	0.83[EUR][1000 genomes]
rs2463434	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2463435	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2468082	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2468083	0.80[EUR][1000 genomes]
rs2468110	0.82[EUR][1000 genomes]
rs2468112	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2565167	0.83[EUR][1000 genomes]
rs2642109	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2642116	0.83[EUR][1000 genomes]
rs2730295	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2731030	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6539167	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs903247	0.83[AMR][1000 genomes];0.86[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	nsv899495	chr12:104990469-105527011	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv899496	chr12:105152391-105199038	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
3	nsv899497	chr12:105155291-105247010	Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2088019	CHST11	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105166200-105166400	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