Variant report

Variant	rs2453594
Chromosome Location	chr17:19484951-19484952
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10735	1.00[CEU][hapmap];0.82[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2120272	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2120273	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2249885	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2440167	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2453595	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2453596	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7212622	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428337	chr17:19340045-19585774	Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
2	nsv482827	chr17:19456848-19645771	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
3	nsv1061408	chr17:19458185-19613357	Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
4	nsv1056125	chr17:19484803-19536116	Enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv1059195	chr17:19484803-19547972	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2453594	COPS3	cis	cerebellum	SCAN
rs2453594	TOM1L2	cis	parietal	SCAN
rs2453594	ALDH3A2	Cis_1M	lymphoblastoid	RTeQTL
rs2453594	CTD-2104P17.1	cis	Nerve Tibial	GTEx
rs2453594	DHRS7B	cis	cerebellum	SCAN
rs2453594	MED9	cis	parietal	SCAN
rs2453594	FLJ10847	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19481200-19485600	Weak transcription	HepG2	liver

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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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