Variant report

Variant	rs1945589
Chromosome Location	chr11:59065162-59065163
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10750912	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10792231	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11229912	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11229914	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11501602	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1945588	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2040326	0.84[CHD][hapmap];0.82[JPT][hapmap]
rs4536240	0.85[ASN][1000 genomes]
rs4939272	0.85[ASN][1000 genomes]
rs7103331	0.85[ASN][1000 genomes]
rs7105556	0.88[ASW][hapmap];0.94[CHB][hapmap];0.84[CHD][hapmap];0.88[JPT][hapmap]
rs7111928	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7121582	0.82[JPT][hapmap]
rs7926943	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7928120	0.82[YRI][hapmap];0.81[EUR][1000 genomes]
rs7945064	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7951053	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050013	chr11:58394598-59221090	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv948365	chr11:58515163-59156405	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	esv3381199	chr11:59015574-59068938	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1046084	chr11:59034871-59314519	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv972924	chr11:59059165-59071373	Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats	TF binding region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1945589	SNORD27	cis	parietal	SCAN
rs1945589	DDB1	cis	parietal	SCAN
rs1945589	FEN1	cis	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:59057200-59066000	Enhancers	Liver	Liver
2	chr11:59064200-59069800	Weak transcription	Pancreas	Pancrea

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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