Variant report

Variant	rs6593538
Chromosome Location	chr1:76898654-76898655
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 9 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs17098942	0.85[CEU][hapmap];0.87[CHB][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4478861	1.00[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4949718	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4949719	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv870621	chr1:76620313-76997071	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv534168	chr1:76718950-77039352	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1006776	chr1:76777323-76899975	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv462006	chr1:76826279-77042405	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
5	nsv546585	chr1:76826279-77042405	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6593538	LRRIQ3	cis	parietal	SCAN
rs6593538	ZNF358	trans	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76896200-76899000	Enhancers	Ovary	ovary
2	chr1:76896400-76899000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr1:76897000-76899200	Weak transcription	Fetal Lung	lung
4	chr1:76898000-76899400	Weak transcription	Fetal Kidney	kidney
5	chr1:76898400-76898800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr1:76898400-76900000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr1:76898600-76898800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:76898600-76899000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr1:76898600-76899400	Enhancers	Brain Substantia Nigra	brain
10	chr1:76898600-76900000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:76898600-76900000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr1:76898600-76900000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

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

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