Variant report

Variant	rs6561443
Chromosome Location	chr13:48772266-48772267
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs12870184	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12875956	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2010173	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561441	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7320402	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7333467	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9526462	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9534971	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9534973	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9534974	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9534976	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9534980	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9534982	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9534985	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9534987	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9562809	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9562811	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9568024	0.81[ASN][1000 genomes]
rs9634814	0.92[EUR][1000 genomes];0.97[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	nsv541766	chr13:48703229-48857639	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	esv3327569	chr13:48743550-48798094	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv1043294	chr13:48762477-48810028	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
4	nsv1031	chr13:48766510-48790172	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6561443	ITM2B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:48764800-48774600	Weak transcription	Duodenum Mucosa	Duodenum
2	chr13:48768400-48773000	Weak transcription	HepG2	liver
3	chr13:48768600-48773200	Weak transcription	Primary T cells fromperipheralblood	blood
4	chr13:48768800-48773600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr13:48768800-48773600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr13:48769000-48772400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr13:48769000-48773000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr13:48769000-48773000	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr13:48769000-48773000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr13:48769000-48773200	Weak transcription	Primary T cells from cord blood	blood
11	chr13:48769000-48773200	Weak transcription	Primary hematopoietic stem cells	blood
12	chr13:48769000-48773600	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr13:48769200-48773000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr13:48769400-48775400	Weak transcription	Primary Natural Killer cells fromperipheralblood	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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