Variant report

Variant	rs1496345
Chromosome Location	chr5:128157526-128157527
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10075560	0.88[ASW][hapmap]
rs10793810	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11745830	0.83[AMR][1000 genomes]
rs11952436	0.87[CEU][hapmap];0.86[JPT][hapmap]
rs12521616	0.83[AMR][1000 genomes]
rs13169056	0.81[AMR][1000 genomes]
rs1363463	0.83[AMR][1000 genomes]
rs1496347	0.81[CEU][hapmap];0.86[JPT][hapmap]
rs1826817	0.83[AMR][1000 genomes]
rs1833549	0.80[CEU][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.81[AMR][1000 genomes]
rs1990919	0.81[AMR][1000 genomes]
rs2522383	0.84[CHD][hapmap]
rs2545024	0.85[JPT][hapmap]
rs7702784	0.81[CEU][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap]

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	nsv1023405	chr5:127955360-128190069	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	esv3392548	chr5:128139102-128159002	Enhancers Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1496345	SLC27A6	cis	parietal	SCAN
rs1496345	SLC12A2	cis	cerebellum	SCAN
rs1496345	CCNI2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:128157400-128157600	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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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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