Variant report

Variant	rs17159863
Chromosome Location	chr7:112311226-112311227
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10228590	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10241709	1.00[CHB][hapmap]
rs10258268	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10275970	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12112671	1.00[CHB][hapmap]
rs17159704	1.00[JPT][hapmap]
rs17159980	1.00[CHB][hapmap];1.00[MEX][hapmap]
rs2204927	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3095043	1.00[JPT][hapmap]
rs4517054	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56391065	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6968530	1.00[CHB][hapmap]
rs73715670	0.93[EUR][1000 genomes]
rs73715673	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73715678	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73715679	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7792951	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531436	chr7:111856171-112585407	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	105 gene(s)	inside rSNPs	diseases
2	nsv889055	chr7:112174089-112353440	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs17159863	LRTM1	trans	brain	seeQTL
rs17159863	GUCA1C	trans	brain	seeQTL
rs17159863	SLC5A7	trans	brain	seeQTL
rs17159863	PDE6H	trans	brain	seeQTL
rs17159863	DAPL1	trans	brain	seeQTL
rs17159863	CRX	trans	brain	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:112308000-112316200	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr7:112309800-112314800	Weak transcription	HSMMtube	muscle
3	chr7:112310000-112317600	Weak 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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