Variant report

Variant	rs12865846
Chromosome Location	chr13:49235277-49235278
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs12430959	0.80[EUR][1000 genomes]
rs12583212	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12583622	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12585234	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12867110	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12867640	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12869467	0.80[EUR][1000 genomes]
rs12870838	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1326697	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1359107	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2148516	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2407247	0.86[ASN][1000 genomes]
rs34119347	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs36088391	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59136233	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7330144	0.80[EUR][1000 genomes]
rs7331325	0.91[EUR][1000 genomes]
rs7334400	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7982278	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7987608	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7988330	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7989251	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9562837	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9562838	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9568067	0.89[EUR][1000 genomes]
rs9568068	0.87[EUR][1000 genomes]
rs9568071	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9568075	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9568079	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9634815	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9634816	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9634817	0.91[EUR][1000 genomes]
rs9742182	0.82[AMR][1000 genomes];0.89[EUR][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12865846	ITM2B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:49229000-49236800	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr13:49229800-49239400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr13:49232200-49235600	Enhancers	Placenta	Placenta
4	chr13:49234000-49235800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr13:49234200-49235400	Enhancers	Primary hematopoietic stem cells short term culture	blood
6	chr13:49234200-49235800	Enhancers	Adipose Nuclei	Adipose
7	chr13:49234400-49235400	Enhancers	Primary B cells from peripheral blood	blood
8	chr13:49234400-49235600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr13:49234400-49235600	Enhancers	Fetal Stomach	stomach
10	chr13:49235000-49235400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr13:49235000-49235400	Enhancers	Monocytes-CD14+_RO01746	blood
12	chr13:49235000-49235800	Enhancers	Primary B cells from cord blood	blood
13	chr13:49235200-49235600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr13:49235200-49235800	Enhancers	GM12878-XiMat	blood
15	chr13:49235200-49236000	Enhancers	Primary neutrophils fromperipheralblood	blood
16	chr13:49235200-49236400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr13:49235200-49238800	Weak transcription	Primary hematopoietic stem cells	blood

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