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Citing CMDGA
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Annotation type
2
variant allelic effects
1
accessible chromatin
Annotation Category
2
Genetic variant effects
1
cis-regulatory elements
Annotation type Category
1
ATAC-seq
Available data
3
bed bed3+
File set status
3
released
Genome assembly (visualization)
3
hg19
1
GRCh38
Organism
3
Homo sapiens
Biosample type
2
cell line
1
primary cell
Biosample term
2
MIN6
1
CD4-positive helper T cell
Date released
2
October, 2022
1
February, 2024
Software used
2546
macs
2386
r
1035
chromhmm
838
encode-ccres
250
abc
136
deltasvm
122
deseq2
114
qTLtools
32
cicero
27
chicago
27
nospecificsoft_customcode
25
seurat
24
gtex_eqtl:V8
24
gtex_finemapping_eQTL:caveman
24
gtex_finemapping_eQTL:caviar
24
gtex_finemapping_eQTL:dapg
18
samtools
15
limix
14
hiccups
14
matrix-eQTL
12
deeptools
12
umitools
11
rasqual
9
salmon
8
fastqtl
6
eigenmt
5
peer
5
unknown
3
mach2qtl
3
minfi
3
sqtlseeker
2
combined S2G strategy
2
emmax
2
mpraflow
1
altius-index
1
bedops
1
betacells_cytokines_t1d
1
bimbam
1
cisgenome
1
e-range
1
epacts
1
fast-lmm
1
haploview
1
pepatac
1
probabel
1
snap
1
spp
Lab
2
AMP-T2D consortium
1
Stephen S. Rich Lab @UVA
Project
2
AMP
1
T1D
RFA
2
AMP
1
T1D
Showing 3 of 3 results
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Download
FileSet
DSR684XQS
released
Annotation file set
: Variant allelic effects annotation for MPRA of the cis-regulatory effects of SNPs associated with T2D and altered in vivo islet chromatin accessibility in MIN6 cells under pathophysiologic endoplasmic reticulum (ER) stress conditions (thapsigargin treatment).
Lab:
AMP-T2D consortium
Project:
AMP
FileSet
DSR646GMS
released
Annotation file set
: Variant allelic effects annotation for MPRA of the cis-regulatory effects of SNPs associated with T2D and altered in vivo islet chromatin accessibility in MIN6 cells under steady state (baseline, DMSO)
Lab:
AMP-T2D consortium
Project:
AMP
FileSet
DSR204EGG
released
Annotation file set
: A canonical set of CD4+ T cell peaks
Lab:
Stephen S. Rich Lab @UVA
Project:
T1D