Variant report

Variant	rs8096564
Chromosome Location	chr18:39910592-39910593
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs12958459	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12958679	0.81[ASN][1000 genomes]
rs1461714	0.90[AFR][1000 genomes]
rs16975918	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16975919	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16975921	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34642158	0.81[ASN][1000 genomes]
rs34802524	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7232300	0.81[ASN][1000 genomes]
rs7232594	0.81[ASN][1000 genomes]
rs7235999	0.87[EUR][1000 genomes]
rs7237280	0.82[ASN][1000 genomes]
rs73469118	0.82[AFR][1000 genomes]
rs8085980	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8090017	0.86[EUR][1000 genomes]
rs9947988	0.81[ASN][1000 genomes]
rs9948169	0.82[ASN][1000 genomes]
rs9959948	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9960132	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949609	chr18:39126941-40070286	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv1059409	chr18:39711099-40139446	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs8096564	PIK3C3	cis	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:39893200-39915200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr18:39909000-39910600	Enhancers	NHDF-Ad	bronchial
3	chr18:39909600-39911000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr18:39909800-39910600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr18:39910000-39910600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr18:39910000-39911600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr18:39910200-39910600	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr18:39910200-39910800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr18:39910400-39916800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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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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