Variant report

Variant	rs12136954
Chromosome Location	chr1:216055493-216055494
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10495007	0.87[JPT][hapmap]
rs11120638	0.93[JPT][hapmap]
rs11120643	0.87[JPT][hapmap]
rs11120659	0.87[JPT][hapmap]
rs11120670	0.88[CHD][hapmap];0.87[JPT][hapmap]
rs11120675	0.81[CHD][hapmap];0.87[JPT][hapmap]
rs11120677	0.88[CHD][hapmap];0.94[JPT][hapmap]
rs12126127	0.88[CHD][hapmap];0.94[JPT][hapmap]
rs12130746	0.81[CHD][hapmap];0.94[JPT][hapmap]
rs12136240	0.93[JPT][hapmap]
rs12733601	1.00[CEU][hapmap];0.88[JPT][hapmap];0.83[AMR][1000 genomes]
rs1934428	0.81[CHD][hapmap];0.94[JPT][hapmap]
rs6658928	0.91[CEU][hapmap]
rs6664028	0.87[JPT][hapmap]
rs7514073	0.94[JPT][hapmap]
rs7536020	0.81[CHD][hapmap];0.87[JPT][hapmap]
rs7544464	0.92[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430324	chr1:215649163-216082605	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv1006504	chr1:215890460-216642124	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv535288	chr1:215890460-216642124	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv949671	chr1:215942740-216120815	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv832548	chr1:215987089-216175724	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv468127	chr1:216054086-216066437	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv549193	chr1:216054086-216066437	Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12136954	BATF3	cis	cerebellum	SCAN
rs12136954	KLHL3	trans	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:216055400-216064200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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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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