Variant report

Variant	rs9888525
Chromosome Location	chr13:49321464-49321465
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs12184704	0.81[ASN][1000 genomes]
rs12184705	0.81[ASN][1000 genomes]
rs17072105	0.81[ASN][1000 genomes]
rs1998511	0.81[ASN][1000 genomes]
rs56959802	0.81[ASN][1000 genomes]
rs57042574	0.81[ASN][1000 genomes]
rs57186324	0.81[ASN][1000 genomes]
rs60424010	0.81[ASN][1000 genomes]
rs6561478	0.85[ASN][1000 genomes]
rs73478310	0.81[ASN][1000 genomes]
rs73478365	0.98[ASN][1000 genomes]
rs9591202	0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs9591203	0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs9591204	0.81[ASN][1000 genomes]
rs9591206	0.85[ASN][1000 genomes]
rs959353	1.00[CHB][hapmap]
rs9595977	0.81[ASN][1000 genomes]
rs9595978	0.81[ASN][1000 genomes]
rs9595988	0.89[EUR][1000 genomes]
rs985466	0.81[ASN][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	nsv1049117	chr13:49089476-49928945	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv832605	chr13:49171305-49344970	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
3	esv2758327	chr13:49283983-49472517	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	esv2759936	chr13:49283983-49472517	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1036621	chr13:49310529-49346405	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1049066	chr13:49316146-49346405	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9888525	ITM2B	cis	lymphoblastoid	seeQTL
rs9888525	RCBTB2	cis	lymphoblastoid	seeQTL

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:49316400-49322200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr13:49317000-49322400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr13:49320800-49322400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr13:49321000-49323400	Weak transcription	Fetal Stomach	stomach
5	chr13:49321400-49322600	Weak transcription	HSMM	muscle
6	chr13:49321400-49322800	Weak transcription	HSMMtube	muscle

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