Variant report

Variant	rs1558697
Chromosome Location	chr7:78092596-78092597
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 7 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs2110872	0.85[JPT][hapmap]
rs2160322	1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7804452	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9649305	0.89[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022764	chr7:77911072-78316607	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1022199	chr7:78054639-78469370	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv538986	chr7:78054639-78469370	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1558697	GTF2IRD1	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:78089600-78093000	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr7:78092000-78092600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr7:78092000-78093600	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr7:78092200-78093400	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr7:78092400-78092600	Genic enhancers	Brain Substantia Nigra	brain
6	chr7:78092400-78093200	Enhancers	HUES6 Cell Line	embryonic stem cell
7	chr7:78092400-78093800	Enhancers	Ovary	ovary

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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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