Variant report

Variant	rs11654880
Chromosome Location	chr17:15024028-15024029
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1076385	0.90[EUR][1000 genomes]
rs2041267	0.93[EUR][1000 genomes]
rs2191115	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2191116	0.93[EUR][1000 genomes]
rs2875084	0.92[EUR][1000 genomes]
rs4427846	0.94[EUR][1000 genomes]
rs4792574	0.93[EUR][1000 genomes]
rs7209181	0.92[EUR][1000 genomes]
rs758485	0.82[EUR][1000 genomes]
rs758489	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs763614	0.87[EUR][1000 genomes]
rs8081018	0.83[EUR][1000 genomes]
rs917538	0.89[EUR][1000 genomes]
rs917539	0.90[EUR][1000 genomes]
rs983292	0.93[EUR][1000 genomes]
rs983293	0.94[EUR][1000 genomes]
rs9913810	0.93[ASN][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	nsv1064686	chr17:14897967-15046005	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1066329	chr17:14983674-15294071	Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
3	nsv543212	chr17:14983674-15294071	Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11654880	ATPAF2	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:15005800-15027000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr17:15021800-15025000	Enhancers	Primary neutrophils fromperipheralblood	blood
3	chr17:15022400-15024200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr17:15022600-15024200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr17:15022600-15024400	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr17:15023200-15026400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr17:15023200-15028600	Enhancers	NHDF-Ad	bronchial
8	chr17:15023400-15024200	Enhancers	H1 Cell Line	embryonic stem cell
9	chr17:15023400-15024400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr17:15023400-15025600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr17:15023400-15028600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr17:15024000-15024200	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr17:15024000-15025000	Enhancers	Gastric	stomach

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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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