Variant report

Variant	rs2288682
Chromosome Location	chr2:54974485-54974486
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs13390196	0.85[AFR][1000 genomes]
rs1510614	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1813272	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1848924	0.88[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1848925	0.85[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2116441	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2288683	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4671972	0.85[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.95[TSI][hapmap]
rs4671975	0.81[AFR][1000 genomes]
rs7567746	0.82[AFR][1000 genomes]
rs7600540	0.86[AFR][1000 genomes]
rs980644	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[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	esv33638	chr2:54765256-55109455	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS 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	29 gene(s)	inside rSNPs	diseases
2	nsv582024	chr2:54894649-54999712	Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1005449	chr2:54938633-55129503	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2288682	CCDC85A	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54967200-54977200	Weak transcription	Pancreas	Pancrea
2	chr2:54969600-54975400	Weak transcription	HepG2	liver
3	chr2:54970400-54974800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr2:54970400-54975600	Weak transcription	Gastric	stomach
5	chr2:54974000-54974600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:54974000-54974600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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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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