Variant report

Variant	rs1980162
Chromosome Location	chr15:58438535-58438536
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11856135	0.81[ASN][1000 genomes]
rs12906402	1.00[ASW][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.90[LWK][hapmap];0.91[MEX][hapmap];1.00[YRI][hapmap]
rs12909201	0.94[ASN][1000 genomes]
rs12913934	0.90[LWK][hapmap];1.00[YRI][hapmap]
rs12916538	1.00[YRI][hapmap]
rs8023564	1.00[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.90[LWK][hapmap];0.86[MEX][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs8035539	1.00[YRI][hapmap];0.80[AFR][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	nsv1038667	chr15:57933076-58481870	Flanking Active TSS Enhancers Genic enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription 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	22 gene(s)	inside rSNPs	diseases
2	nsv542400	chr15:57933076-58481870	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv1047246	chr15:58375607-58707158	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv457172	chr15:58417895-58457507	Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv569597	chr15:58417895-58457507	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1980162	AQP9	cis	cerebellum	SCAN
rs1980162	BCL2L10	cis	parietal	SCAN
rs1980162	TCF12	cis	cerebellum	SCAN
rs1980162	LOC654342	trans	parietal	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:58433000-58438800	Weak transcription	NHDF-Ad	bronchial
2	chr15:58433400-58441800	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr15:58433800-58442400	Weak transcription	Aorta	Aorta
4	chr15:58436400-58439400	Active TSS	Primary B cells from cord blood	blood
5	chr15:58437600-58438800	Active TSS	Primary hematopoietic stem cells	blood
6	chr15:58437800-58439400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
7	chr15:58438200-58438800	Enhancers	Primary neutrophils fromperipheralblood	blood
8	chr15:58438200-58441800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr15:58438400-58438800	Weak transcription	Liver	Liver
10	chr15:58438400-58440000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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