Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Biological constraints on GWAS SNPs at suggestive significance thresholds reveal true BMI loci [hMSC_adipocytes_captureC]

ABSTRACT: We investigated whether intersecting functional genomic data (ATAC-seq + promoter focused Capture C) with increasingly powered publically available GWAS for Body Mass Index and Waist to Hip Ratio could identify additional true postiive subsignficant signals (5x10-8< P value < 5x10-4) without increasing the GWAS sample size

ORGANISM(S): Homo sapiens

PROVIDER: GSE164911 | GEO | 2021/01/16

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Biological constraints on GWAS SNPs at suggestive significance thresholds reveal true BMI loci [hMSC_adipocytes_atacseq]

Project description:We investigated whether intersecting functional genomic data (ATAC-seq + promoter focused Capture C) with increasingly powered publically available GWAS for Body Mass Index and Waist to Hip Ratio could identify additional true postiive subsignficant signals (5x10-8< P value < 5x10-4) without increasing the GWAS sample size

2021-01-16 | GSE164745 | GEO

Biological constraints on GWAS SNPs at suggestive significance thresholds reveal true BMI loci.

Project description:This SuperSeries is composed of the SubSeries listed below.

2021-01-15 | GSE164912 | GEO

Biological constraints on GWAS SNPs at suggestive significance thresholds reveal true BMI loci.

Project description:Biological constraints on GWAS SNPs at suggestive significance thresholds reveal true BMI loci.

| PRJNA692436 | ENA

Biological constraints on GWAS SNPs at suggestive significance thresholds reveal true BMI loci [hMSC_adipocytes_captureC]

Project description:Biological constraints on GWAS SNPs at suggestive significance thresholds reveal true BMI loci [hMSC_adipocytes_captureC]

| PRJNA692438 | ENA

Biological constraints on GWAS SNPs at suggestive significance thresholds reveal true BMI loci [hMSC_adipocytes_atacseq]

Project description:Biological constraints on GWAS SNPs at suggestive significance thresholds reveal true BMI loci [hMSC_adipocytes_atacseq]

| PRJNA691887 | ENA

Biological constraints on GWAS SNPs at suggestive significance thresholds reveal additional BMI loci.

Project description: Not available

| S-EPMC7815306 | biostudies-literature

Open chromatin profiling in adipose tissue marks genomic regions with functional roles in cardiometabolic traits

Project description:Identifying the regulatory mechanisms of genome-wide association study (GWAS) loci affecting adipose tissue has been restricted due to limited characterization of adipose transcriptional regulatory elements. We profiled chromatin accessibility in three frozen human subcutaneous adipose tissue needle biopsies and preadipocytes and adipocytes from the Simpson Golabi-Behmel Syndrome (SGBS) cell strain using an assay for transposase-accessible chromatin (ATAC-seq). We identified 68,571 representative accessible chromatin regions (peaks) across adipose tissue samples (FDR<5%). GWAS loci for eight cardiometabolic traits were enriched in these peaks (p<0.005), with the strongest enrichment for waist-hip ratio. Of 110 recently described cardiometabolic GWAS loci colocalized with adipose tissue eQTLs, 59 loci had one or more variants overlapping an adipose tissue peak. Annotated variants at the SNX10 waist-hip ratio locus and the ATP2A1-SH2B1 body mass index locus showed allelic differences in regulatory assays. These adipose tissue accessible chromatin regions elucidate genetic variants that may alter adipose tissue function to impact cardiometabolic traits.

2019-01-01 | GSE110734 | GEO

Ethnic-specific BMI and waist circumference thresholds.

Project description: Not available

| S-EPMC3933952 | biostudies-literature

Evidence for correlations between BMI-associated SNPs and circRNAs.

Project description: Not available

| S-EPMC9314347 | biostudies-literature

Prostate Cancer Risk SNPs in Androgen Receptor Target Sites

Project description:We profiled androgen receptor (AR) genomic targets using high-throughput sequencing of chromatin-immunoprecipitated (ChIP) DNA from TMPRSS2-ERG fusion gene positive DUCaP prostate cancer cells. ChIp-seq and microarray gene expression profiling datasets were integrated with the NHGRI GWAS PCa risk SNPs catalog to identify disease susceptibility SNPs localized within functional androgen receptor binding sites (ARBSs). Eighty GWAS index or linked SNPs were found to be localized in ARBSs. Among these rs11891426:T>G in the 7th intron of the melanophilin gene was found located within a novel putative auxiliary AR binding motif, which we found enriched in the neighborhood of canonical androgen responsive elements. T→G exchange attenuated the transcriptional activity of the ARBS in an AR reporter gene assay of prostate cancer cell models. It went also in line with decreased melanophilin protein level in primary prostate tumors with G allele.These results unravel a hidden link between androgen receptor and a functional PCa risk SNP, whose allele alteration affects androgen regulation of its host gene melanophilin . Genomic profile of androgen receptor binding sites of androgen or vehicle treated DUCaP cells using ChIP-seq. IgG precipiated DNAs from both treatments served as controls.

2015-07-10 | E-GEOD-70679 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data