Variant report

Variant	rs9562828
Chromosome Location	chr13:49177989-49177990
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1009717	0.82[AMR][1000 genomes]
rs1009718	0.82[AMR][1000 genomes]
rs12859099	0.81[EUR][1000 genomes]
rs1575920	0.82[AMR][1000 genomes]
rs1854017	0.82[AMR][1000 genomes]
rs1887152	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1887154	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2407093	0.80[ASN][1000 genomes]
rs4497565	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7325719	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7332322	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7990619	0.82[AMR][1000 genomes]
rs7990660	0.82[AMR][1000 genomes]
rs9568051	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9568056	0.82[AMR][1000 genomes]
rs9568058	0.82[AMR][1000 genomes]
rs9568061	0.82[AMR][1000 genomes]
rs9568062	0.82[AMR][1000 genomes]
rs9595937	0.90[EUR][1000 genomes];0.97[ASN][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	nsv1041275	chr13:49045566-49242357	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers 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	14 gene(s)	inside rSNPs	diseases
2	nsv541769	chr13:49045566-49242357	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv832604	chr13:49061081-49281807	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	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
5	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9562828	ITM2B	Cis_1M	lymphoblastoid	RTeQTL
rs9562828	LPAR6	cis	parietal	SCAN
rs9562828	ITM2B	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:49174600-49178000	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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