Variant report

Variant	rs9901291
Chromosome Location	chr17:17541750-17541751
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11078392	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11869492	0.81[ASN][1000 genomes]
rs12449964	0.81[CEU][hapmap]
rs12453926	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12936587	0.81[CEU][hapmap]
rs4646340	0.80[JPT][hapmap]
rs4646342	0.84[JPT][hapmap]
rs4925062	0.82[AMR][1000 genomes]
rs62066209	0.81[ASN][1000 genomes]
rs7213809	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7218582	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7219757	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7225141	0.83[MEX][hapmap]
rs8074794	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8076796	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9783803	0.82[AMR][1000 genomes]
rs9890064	1.00[CEU][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9891340	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv907748	chr17:17412032-17782404	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription 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	89 gene(s)	inside rSNPs	diseases
2	nsv1065270	chr17:17430116-17823086	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
3	nsv543236	chr17:17430116-17823086	Bivalent Enhancer Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
4	nsv833384	chr17:17491483-17645648	Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
5	nsv869118	chr17:17509896-17599850	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv907751	chr17:17530554-17581184	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9901291	LRRC48	cis	cerebellum	SCAN
rs9901291	TOM1L2	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17528800-17543400	Weak transcription	Spleen	Spleen
2	chr17:17537200-17541800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr17:17537200-17541800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr17:17539600-17543000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr17:17540000-17545000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr17:17540200-17542000	Enhancers	Monocytes-CD14+_RO01746	blood
7	chr17:17540200-17543200	Weak transcription	Adipose Nuclei	Adipose
8	chr17:17541000-17545400	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr17:17541200-17542200	Weak transcription	Fetal Lung	lung
10	chr17:17541200-17545000	Weak transcription	Fetal Stomach	stomach
11	chr17:17541600-17542200	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr17:17541600-17542400	Enhancers	HMEC	breast
13	chr17:17541600-17545400	Enhancers	Primary neutrophils fromperipheralblood	blood

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

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