Variant report

Variant	rs13003076
Chromosome Location	chr2:48616567-48616568
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10153773	0.91[ASN][1000 genomes]
rs10174717	0.82[ASN][1000 genomes]
rs10199431	0.84[ASN][1000 genomes]
rs11676168	0.82[ASN][1000 genomes]
rs13385535	0.82[ASN][1000 genomes]
rs28841370	0.87[ASN][1000 genomes]
rs4411759	0.81[ASN][1000 genomes]
rs56352447	0.81[ASN][1000 genomes]
rs57668696	0.85[ASN][1000 genomes]
rs58660534	0.87[ASN][1000 genomes]
rs59761994	0.87[ASN][1000 genomes]
rs62136987	0.87[ASN][1000 genomes]
rs62137001	0.87[ASN][1000 genomes]
rs62137002	0.87[ASN][1000 genomes]
rs62137003	0.87[ASN][1000 genomes]
rs62137005	0.87[ASN][1000 genomes]
rs62137006	0.87[ASN][1000 genomes]
rs62137007	0.87[ASN][1000 genomes]
rs62137008	0.84[ASN][1000 genomes]
rs62137009	0.84[ASN][1000 genomes]
rs6545030	0.82[ASN][1000 genomes]
rs6545034	0.85[ASN][1000 genomes]
rs6545035	0.85[ASN][1000 genomes]
rs6712029	0.82[ASN][1000 genomes]
rs72820405	0.87[ASN][1000 genomes]
rs7574125	0.92[ASN][1000 genomes]
rs9309152	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530831	chr2:48059709-48632317	Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers 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	30 gene(s)	inside rSNPs	diseases
2	nsv874001	chr2:48534363-48624007	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	12 gene(s)	inside rSNPs	diseases
3	esv2762252	chr2:48554150-48741093	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv874003	chr2:48570509-48619869	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13003076	STON1,GTF2A1L,FLJ46838,STON1-GTF2A1L	cis	brain	BrainEAC

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48608400-48618000	Weak transcription	Brain Cingulate Gyrus	brain
2	chr2:48614800-48618400	Weak transcription	Brain Substantia Nigra	brain
3	chr2:48615600-48616800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood

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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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