Variant report

Variant	rs7787781
Chromosome Location	chr7:78069787-78069788
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10237632	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs10260177	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs10270014	0.96[EUR][1000 genomes]
rs10485888	0.94[TSI][hapmap]
rs1157211	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs59417246	0.86[EUR][1000 genomes]
rs73148390	0.86[EUR][1000 genomes]
rs7779438	0.85[EUR][1000 genomes]
rs7786447	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs7791794	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs7798901	0.94[TSI][hapmap]
rs7801864	0.86[EUR][1000 genomes]
rs7802215	0.84[MEX][hapmap]
rs7803197	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7787781	GTF2IRD1	cis	cerebellum	SCAN
rs7787781	PHTF2	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:78067000-78072400	Weak transcription	Brain Cingulate Gyrus	brain
2	chr7:78067000-78079800	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr7:78067600-78071600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr7:78068000-78071000	Weak transcription	Brain Anterior Caudate	brain
5	chr7:78068400-78069800	Weak transcription	Fetal Brain Female	brain
6	chr7:78068400-78071000	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr7:78068600-78071200	Weak transcription	Brain Angular Gyrus	brain
8	chr7:78068600-78071400	Weak transcription	Brain Substantia Nigra	brain
9	chr7:78068800-78071200	Weak transcription	Brain Hippocampus Middle	brain
10	chr7:78069000-78071400	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr7:78069200-78070200	Weak transcription	Pancreatic Islets	Pancreatic Islet

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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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