Variant report

Variant	rs2399638
Chromosome Location	chr11:93018077-93018078
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10765598	0.82[EUR][1000 genomes]
rs10765600	0.90[EUR][1000 genomes]
rs10765601	0.89[EUR][1000 genomes]
rs10765603	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs10831019	0.89[EUR][1000 genomes]
rs10831020	0.90[EUR][1000 genomes]
rs10831024	0.83[EUR][1000 genomes]
rs10831025	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs11020243	0.89[EUR][1000 genomes]
rs11020246	0.89[EUR][1000 genomes]
rs11020263	0.83[EUR][1000 genomes]
rs11020267	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11020270	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs12364612	0.84[CEU][hapmap];0.80[EUR][1000 genomes]
rs12419719	0.84[CEU][hapmap]
rs12790059	0.84[CEU][hapmap]
rs12792270	0.82[EUR][1000 genomes]
rs12807018	0.82[EUR][1000 genomes]
rs12807308	0.84[CEU][hapmap]
rs12807762	0.84[CEU][hapmap]
rs4132359	0.84[CEU][hapmap];0.80[EUR][1000 genomes]
rs4301752	0.88[EUR][1000 genomes]
rs4753455	0.80[EUR][1000 genomes]
rs7107679	0.84[CEU][hapmap];0.80[EUR][1000 genomes]
rs7110891	0.89[EUR][1000 genomes]
rs7114042	0.89[EUR][1000 genomes]
rs7122184	0.89[EUR][1000 genomes]
rs7122837	0.88[EUR][1000 genomes]
rs7126901	0.84[CEU][hapmap];0.80[EUR][1000 genomes]
rs7936149	0.89[EUR][1000 genomes]
rs7950862	0.89[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	nsv1039134	chr11:92790000-93219942	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	esv1807162	chr11:93013387-93022144	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
3	nsv555905	chr11:93018077-93022144	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2399638	FAT3	cis	parietal	SCAN
rs2399638	SLC36A4	cis	parietal	SCAN
rs2399638	CCDC67	cis	cerebellum	SCAN
rs2399638	NOX4	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:93016600-93020600	Weak transcription	GM12878-XiMat	blood

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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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