Variant report

Variant	rs1055409
Chromosome Location	chr6:87795310-87795311
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1998617	0.95[CEU][hapmap];0.85[MEX][hapmap];0.96[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6909630	0.95[CEU][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6910649	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7738290	0.94[CEU][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7745823	0.85[CHB][hapmap];0.87[EUR][1000 genomes]
rs7748510	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9294363	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9344675	0.95[CEU][hapmap];0.92[MEX][hapmap];0.96[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9362387	0.80[EUR][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	nsv1024751	chr6:87433199-87908721	Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv5385	chr6:87781015-87803663	Enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	esv1002835	chr6:87792224-87800627	Enhancers Weak transcription Active TSS Strong transcription	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1055409	C6orf165	cis	parietal	SCAN
rs1055409	C6orf162	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:87793000-87798200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr6:87793200-87797600	Weak transcription	GM12878-XiMat	blood
3	chr6:87794000-87799800	Strong transcription	Placenta	Placenta

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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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