Variant report

Variant	rs780060
Chromosome Location	chr2:125135372-125135373
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10496629	0.83[CEU][hapmap];0.89[GIH][hapmap];0.81[TSI][hapmap]
rs1946552	0.95[CHB][hapmap];0.91[JPT][hapmap];0.81[LWK][hapmap];0.90[YRI][hapmap]
rs1946553	0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap]
rs2565761	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs2584358	0.80[ASN][1000 genomes]
rs720477	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs779981	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap]
rs779998	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs779999	0.85[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs780045	0.91[CEU][hapmap];0.86[CHB][hapmap];0.85[GIH][hapmap];0.92[MEX][hapmap];0.90[TSI][hapmap]
rs780046	0.91[CEU][hapmap];0.86[CHB][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs780057	0.90[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap]
rs780059	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs796641	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs811902	0.80[GIH][hapmap];0.83[MEX][hapmap];0.93[MKK][hapmap];0.81[TSI][hapmap]

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	nsv874989	chr2:124892592-125176030	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv1014610	chr2:125124983-125350342	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
3	nsv834355	chr2:125128585-125291043	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs780060	GLI2	cis	parietal	SCAN

Chromatin state (count:0 , 50 per page) page:

No data

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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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