Variant report

Variant	rs12594013
Chromosome Location	chr15:75596353-75596354
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11634109	0.88[EUR][1000 genomes]
rs12591309	0.86[CHB][hapmap]
rs12592505	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs12593372	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs12593870	0.93[CHB][hapmap];0.89[JPT][hapmap]
rs1809714	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1984586	0.94[EUR][1000 genomes]
rs1984587	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3803466	0.81[JPT][hapmap]
rs3866545	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4310817	0.93[EUR][1000 genomes]
rs4886684	0.92[EUR][1000 genomes]
rs4886697	0.92[CHB][hapmap];0.89[JPT][hapmap]
rs55653892	0.96[EUR][1000 genomes]
rs56164452	0.93[EUR][1000 genomes]
rs59084522	0.96[EUR][1000 genomes]
rs7164167	0.95[EUR][1000 genomes]
rs7164429	0.89[CEU][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs7166436	0.90[EUR][1000 genomes]
rs7166852	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7167401	0.94[EUR][1000 genomes]
rs7183520	0.94[EUR][1000 genomes]
rs73435015	0.96[EUR][1000 genomes]
rs73435089	0.94[EUR][1000 genomes]
rs73436803	0.93[EUR][1000 genomes]
rs8031650	0.94[EUR][1000 genomes]
rs9673084	0.92[EUR][1000 genomes]

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	nsv1039713	chr15:75394213-75674389	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv1037713	chr15:75401213-75665304	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
3	nsv833056	chr15:75452947-75614590	Enhancers Strong transcription Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	nsv482859	chr15:75493899-75688451	Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
5	nsv1035829	chr15:75504534-75692417	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
6	nsv977736	chr15:75509295-75632679	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
7	esv3332853	chr15:75538752-75607377	Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs12594013	MAN2C1	cis	Whole Blood	GTEx
rs12594013	MAN2C1	cis	Esophagus Muscularis	GTEx
rs12594013	RCN2	cis	cerebellum	SCAN
rs12594013	SEMA7A	cis	cerebellum	SCAN
rs12594013	NEIL1	cis	cerebellum	SCAN
rs12594013	SNUPN	cis	parietal	SCAN
rs12594013	MAN2C1	cis	parietal	SCAN

Chromatin state (count:0 , 50 per page) page:

No data

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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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