Variant report

Variant	rs17025528
Chromosome Location	chr1:216043153-216043154
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10495008	1.00[CEU][hapmap]
rs1325525	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1575757	1.00[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.92[JPT][hapmap];0.89[TSI][hapmap]
rs1578207	1.00[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];0.92[JPT][hapmap];0.90[TSI][hapmap];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17025482	1.00[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];0.92[JPT][hapmap];0.90[TSI][hapmap];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17025486	1.00[CHB][hapmap];0.92[JPT][hapmap];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17025517	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17025539	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.94[LWK][hapmap];0.82[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap]
rs17042183	1.00[CHB][hapmap];0.83[JPT][hapmap]
rs4129021	1.00[CHB][hapmap];0.92[JPT][hapmap];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4353061	1.00[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.92[JPT][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4417038	1.00[CHB][hapmap];0.92[JPT][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57274121	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59708254	0.82[ASN][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	nsv430324	chr1:215649163-216082605	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv1006504	chr1:215890460-216642124	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv535288	chr1:215890460-216642124	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv949671	chr1:215942740-216120815	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv832548	chr1:215987089-216175724	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17025528	CXCL11	trans	brain	seeQTL
rs17025528	SF1	trans	brain	seeQTL
rs17025528	SCGN	trans	brain	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:216042600-216043400	Enhancers	Adipose Derived Mesenchymal Stem Cell 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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