Variant report

Variant	rs7539781
Chromosome Location	chr1:90856246-90856247
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs6657163	0.89[AFR][1000 genomes]
rs7549917	0.95[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1000787	chr1:90809476-90874481	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
2	esv3394726	chr1:90811671-91019675	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	esv1801569	chr1:90819992-90983299	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	esv1808806	chr1:90819992-90983299	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
5	esv1822918	chr1:90819992-90983299	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
6	esv1850863	chr1:90819992-90983299	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	esv2757740	chr1:90819992-90983299	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
8	esv2758949	chr1:90819992-90983299	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
9	nsv427697	chr1:90819992-90983299	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
10	nsv428124	chr1:90819992-90983299	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
11	esv1811797	chr1:90819992-91008105	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	nsv432487	chr1:90824652-90931765	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7539781	LRTM1	trans	brain	seeQTL
rs7539781	SLC5A7	trans	brain	seeQTL
rs7539781	GUCA1C	trans	brain	seeQTL
rs7539781	SH2D2A	trans	brain	seeQTL
rs7539781	SERPINA1	trans	lymphoblastoid	seeQTL
rs7539781	BCR	trans	lymphoblastoid	seeQTL

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:90853200-90858600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:90853600-90856400	Weak transcription	NH-A	brain
3	chr1:90853600-90856400	Weak transcription	NHEK	skin
4	chr1:90853600-90858600	Weak transcription	HMEC	breast
5	chr1:90853600-90858600	Weak transcription	HSMM	muscle
6	chr1:90853800-90856600	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr1:90853800-90858800	Weak transcription	Osteobl	bone
8	chr1:90854200-90856600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr1:90854200-90856600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr1:90854200-90856800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr1:90854200-90857600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr1:90854200-90861200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr1:90854400-90868200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr1:90856200-90857000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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