Variant report

Variant	rs6493676
Chromosome Location	chr15:54640382-54640383
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11856987	1.00[JPT][hapmap]
rs1397998	1.00[JPT][hapmap]
rs1397999	1.00[JPT][hapmap]
rs1398003	1.00[JPT][hapmap]
rs1511795	1.00[JPT][hapmap]
rs16973458	1.00[JPT][hapmap]
rs16974513	1.00[JPT][hapmap]
rs487588	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs498529	0.80[CEU][hapmap]
rs522021	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs562918	0.81[ASW][hapmap]
rs563881	0.95[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs564119	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs567422	1.00[CHB][hapmap]
rs572288	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs573740	0.85[CEU][hapmap];0.85[GIH][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes]
rs7182182	1.00[JPT][hapmap]
rs8031781	0.85[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.93[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	nsv817539	chr15:54132584-55095235	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	esv1845471	chr15:54556063-54685463	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv974495	chr15:54639855-54641537	Weak transcription	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6493676	PMPCA	trans	cerebellum	SCAN
rs6493676	SCG3	cis	parietal	SCAN
rs6493676	DMXL2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:54547000-54652600	Weak transcription	Fetal Lung	lung

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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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