Variant report

Variant	rs4886755
Chromosome Location	chr15:76298132-76298133
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10444856	0.96[CEU][hapmap];0.86[YRI][hapmap];0.89[EUR][1000 genomes]
rs10851884	0.93[ASW][hapmap];0.96[CEU][hapmap];0.93[TSI][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11072562	0.82[EUR][1000 genomes]
rs11072566	0.93[ASW][hapmap];0.89[CEU][hapmap];0.97[LWK][hapmap];0.94[MKK][hapmap];0.89[TSI][hapmap];0.85[YRI][hapmap];0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11072567	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11636251	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12437816	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12593806	0.80[EUR][1000 genomes]
rs1874953	0.93[ASW][hapmap];0.96[CEU][hapmap];0.81[LWK][hapmap];0.93[TSI][hapmap];0.86[YRI][hapmap];0.90[EUR][1000 genomes]
rs1976748	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs2088599	0.85[EUR][1000 genomes]
rs2201917	0.86[EUR][1000 genomes]
rs28525382	0.81[EUR][1000 genomes]
rs28550045	0.80[EUR][1000 genomes]
rs28607641	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4886466	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4886748	0.80[ASW][hapmap];0.92[CEU][hapmap];0.84[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7177266	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8027685	0.88[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	nsv531903	chr15:75889302-76342128	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	nsv1053717	chr15:76196674-76314542	Weak transcription Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1040053	chr15:76197988-76314542	Genic enhancers Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv904398	chr15:76220285-76359055	Enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv569998	chr15:76232605-76550938	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv1042140	chr15:76243040-76298555	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv542437	chr15:76243040-76298555	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4886755	NRG4	cis	parietal	SCAN
rs4886755	NRG4	cis	cerebellum	SCAN
rs4886755	UBE2Q2	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:76290400-76304000	Weak transcription	Pancreas	Pancrea
2	chr15:76291400-76303800	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr15:76295200-76303200	Weak transcription	Stomach Mucosa	stomach
4	chr15:76295400-76302000	Weak transcription	Hela-S3	cervix
5	chr15:76297600-76300800	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr15:76298000-76298200	Enhancers	Monocytes-CD14+_RO01746	blood
7	chr15:76298000-76299200	Enhancers	Primary neutrophils fromperipheralblood	blood
8	chr15:76298000-76299400	Enhancers	Primary hematopoietic stem cells short term culture	blood

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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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