Variant report

Variant	rs12913242
Chromosome Location	chr15:46131925-46131926
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10153018	0.84[EUR][1000 genomes]
rs10153045	0.84[EUR][1000 genomes]
rs11635633	0.84[EUR][1000 genomes]
rs11638402	0.84[EUR][1000 genomes]
rs11638436	0.84[EUR][1000 genomes]
rs34042928	0.83[EUR][1000 genomes]
rs34965865	0.83[EUR][1000 genomes]
rs35545352	0.80[ASN][1000 genomes]
rs4774812	0.84[EUR][1000 genomes]
rs4774817	0.83[EUR][1000 genomes]
rs62007671	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6493178	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904189	chr15:45821158-46298458	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv904191	chr15:45902779-46381874	Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	nsv523136	chr15:45990780-46158407	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv904192	chr15:46052390-46266488	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
5	nsv1048473	chr15:46053924-46410639	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv542373	chr15:46053924-46410639	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv1052030	chr15:46086870-46255118	Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
8	nsv1037524	chr15:46098040-46138427	Enhancers Active TSS Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv1038457	chr15:46111452-46258188	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12913242	SNAP23	cis	cerebellum	SCAN
rs12913242	LTK	cis	parietal	SCAN
rs12913242	PLA2G4D	cis	cerebellum	SCAN
rs12913242	NUSAP1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:46122800-46133000	Weak transcription	Pancreas	Pancrea
2	chr15:46130200-46133600	Weak transcription	Fetal Brain Male	brain

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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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