chr19:1040102-1065571

25469 bp

More information

1 gene is contained within or overlaps this genomic region:

Genomic Context

The genome browser snapshot is fully interactive. Mouse over track elements for more information. Click and drag to move tracks. Click and drag on top positional guide to zoom to a sub-region.

To add tracks, use the provided link to switch to the full genome browser view.

Genetic Variation and Variant-based Trait Associations (GWAS)

Variants contained within the region chr19:1040102-1065571.

Back to Top

4,270 variant records to (corresponding to 3,818 unique genomic positions) are contained within the region chr19:1040102-1065571.

Of these, the following were found to have genome-wide significance in a NIAGADS dataset or the NHGRI GWAS Catalog:

NIAGADS: Alzheimer's Disease

NIAGADS AD GWAS summary statistics datasets in which colocated variants have a genome-wide significance supported by a p-value ≤ 5 x 10-8.

For exome array studies, a cutoff of p-value < 1 x 10-3 was used.

Click on accession numbers to view a detailed report about the dataset or to request access to the data.

Back to Top

Login in to select variants and add them to your basket.

Variant Allele p-Value Track Accession
A 1.1e-15 IGAP 2013: Stages 1 and 2 NG00036
G 1.4e-15 IGAP 2013: Stages 1 and 2 NG00036
G 4.2e-13 IGAP 2013: Stages 1 and 2 NG00036
G 5.2e-13 IGAP 2013: Stages 1 and 2 NG00036
G 1.9e-12 IGAP 2013: Stages 1 and 2 NG00036
A 5.5e-12 IGAP 2013: Stages 1 and 2 NG00036
T 4.9e-11 IGAP 2013: Stages 1 and 2 NG00036
G 1.5e-9 IGAP 2013: Stages 1 and 2 NG00036
A 1.7e-9 IGAP 2013: Stage 1 NG00036
A 2.2e-9 ADGC African Americans 2013: APOE Adj NG00039
G 4.3e-9 IGAP 2013: Stage 1 NG00036
A 4.7e-9 IGAP 2013: Stage 1 NG00036
C 9.2e-9 IGAP 2013: Stages 1 and 2 NG00036
G 1.2e-8 IGAP 2013: Stage 1 NG00036
G 1.3e-8 IGAP 2013: Stage 1 NG00036
G 1.3e-8 IGAP 2013: Stage 1 NG00036
T 1.7e-8 IGAP 2013: Stage 1 NG00036
A 1.8e-8 IGAP 2013: Stage 1 NG00036
G 2.0e-8 IGAP 2013: Stages 1 and 2 NG00036

NHGRI: Alzheimer's Disease

Alzheimer's Disease-related annotations for the dbSNP refSNPs contained within this region in the NHGRI GWAS Catalog.

Back to Top

Login in to select variants and add them to your basket.

Variant Allele Frequency p-Value Odds Ratio/Beta Trait EFO Study Design Study
? 0.100 5.0e-17 1.23 Alzheimers disease EFO_0000249 13,182 European ancestry cases, 26,161 European ancestry controls Common variants at ABCA7, MS4A6A/MS4A4E, EPHA1, CD33 and CD2AP are associated with Alzheimer's disease. PMID: 21460840
A 0.190 1.0e-15 1.15 Alzheimers disease EFO_0000249 8,572 European ancestry cases, 11,312 European ancestry controls Meta-analysis of 74,046 individuals identifies 11 new susceptibility loci for Alzheimer's disease. PMID: 24162737
G 0.070 2.0e-9 1.79 Alzheimers disease EFO_0000249 N/A Variants in the ATP-binding cassette transporter (ABCA7), apolipoprotein E ϵ4,and the risk of late-onset Alzheimer disease in African Americans. PMID: 23571587
G 0.190 6.0e-7 1.15 Alzheimers disease EFO_0000249 10,523 European ancestry cases, 28,231 European ancestry controls Common variants at MS4A4/MS4A6E, CD2AP, CD33 and EPHA1 are associated with late-onset Alzheimer's disease. PMID: 21460841

NIAGADS: Related neuropathologies and AD biomarkers

NIAGADS AD GWAS summary statistics datasets in which colocated variants have a genome-wide significance supported by a p-value ≤ 5 x 10-8.

For exome array studies, a cutoff of p-value < 1 x 10-3 was used.

Click on accession numbers to view a detailed report about the dataset or to request access to the data.

NHGRI: Other Traits (incl. related neuropathologies and AD biomarkers)

Trait associations for the dbSNP refSNP contained with this region in the NHGRI GWAS Catalog.

Functional Genomics

Genomic regions associated with significant scores or peaks in a functional genomics anlaysis that are located within this span.

See the documentation documentation for more information on the functional genomics tracks.

Back to Top

To view functional genomics annotations on the genome browser, first select tracks in the table below and then use the provided button to load the tracks on the browser.

Track #Hits Characteristics Track Type Platform
H3K4me1 HM ChIP-seq on human NH-A
3 histone peak ChIP-seq
H4K20me1 HM ChIP-seq on human NH-A
2 histone peak ChIP-seq
H3K27me3 HM ChIP-seq on human NH-A
1 histone peak ChIP-seq
H3K9ac HM ChIP-seq on human NH-A
1 histone peak ChIP-seq
H3K4me2 HM ChIP-seq on human NH-A
1 histone peak ChIP-seq
H3K4me3 HM ChIP-seq on human NH-A
1 histone peak ChIP-seq
H3K9me3 HM ChIP-seq on human NH-A
1 histone peak ChIP-seq
CTCF TFBS ChIP-seq on human BE2-C
3 transcription factor binding site ChIP-seq
CTCF TFBS ChIP-seq on human Gliobla
2 transcription factor binding site ChIP-seq
POLR2A TFBS ChIP-seq on human Gliobla
2 transcription factor binding site ChIP-seq
FOXP2 TFBS ChIP-seq on human SK-N-MC
2 transcription factor binding site ChIP-seq
POLR2A TFBS ChIP-seq on human U87
1 transcription factor binding site ChIP-seq
POLR2A TFBS ChIP-seq on human SK-N-SH
1 transcription factor binding site ChIP-seq
CTCF TFBS ChIP-seq on human NH-A
1 transcription factor binding site ChIP-seq
CTCF TFBS ChIP-seq on human SK-N-SH_RA
1 transcription factor binding site ChIP-seq
REST TFBS ChIP-seq on human U87
1 transcription factor binding site ChIP-seq
CTCF TFBS ChIP-seq on human HA-sp
1 transcription factor binding site ChIP-seq
USF1 TFBS ChIP-seq on human SK-N-SH_RA
1 transcription factor binding site ChIP-seq
CTCF TFBS ChIP-seq on human SK-N-SH_RA
1 transcription factor binding site ChIP-seq
CTCF TFBS ChIP-seq on human HBMEC
1 transcription factor binding site ChIP-seq
FOXP2 TFBS ChIP-seq on human PFSK-1
1 transcription factor binding site ChIP-seq
RAD21 TFBS ChIP-seq on human SK-N-SH_RA
1 transcription factor binding site ChIP-seq
DNase-seq on human Medullo
9 DNAse hypersensitive region DNase-Hypersensitivity seq
DNase-seq on human SK-N-MC
9 DNAse hypersensitive region DNase-Hypersensitivity seq
DNase-seq on human BE2-C
9 DNAse hypersensitive region DNase-Hypersensitivity seq
DNase-seq on human Gliobla
6 DNAse hypersensitive region DNase-Hypersensitivity seq
DNase-seq on human SK-N-SH_RA
6 DNAse hypersensitive region DNase-Hypersensitivity seq
DNase-seq on human HBMEC
5 DNAse hypersensitive region DNase-Hypersensitivity seq
DNase-seq on human HA-h
5 DNAse hypersensitive region DNase-Hypersensitivity seq
DNase-seq on human NH-A
4 DNAse hypersensitive region DNase-Hypersensitivity seq
DNase-seq on human HA-sp
3 DNAse hypersensitive region DNase-Hypersensitivity seq