Variant report

Variant	rs1359107
Chromosome Location	chr13:49232598-49232599
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1009719	0.82[ASN][1000 genomes]
rs12050047	0.82[ASN][1000 genomes]
rs12583212	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12583622	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12585234	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12864882	0.84[ASN][1000 genomes]
rs12865846	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12867110	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12867640	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12870838	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12870872	0.81[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs12871411	0.81[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs12871822	0.81[ASN][1000 genomes]
rs12876715	0.81[ASN][1000 genomes]
rs1326697	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1980838	0.82[ASN][1000 genomes]
rs1980839	0.82[ASN][1000 genomes]
rs2146861	0.82[ASN][1000 genomes]
rs2148516	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34119347	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs36088391	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59136233	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59927903	0.81[ASN][1000 genomes]
rs7331325	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7334400	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7982278	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7987608	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7988330	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7989251	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9535055	0.82[ASN][1000 genomes]
rs9535056	0.82[ASN][1000 genomes]
rs9535058	0.84[ASN][1000 genomes]
rs9535061	0.81[AFR][1000 genomes]
rs9562835	0.92[ASN][1000 genomes]
rs9562836	0.92[ASN][1000 genomes]
rs9562837	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9562838	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9568057	0.82[ASN][1000 genomes]
rs9568060	0.82[ASN][1000 genomes]
rs9568063	0.82[ASN][1000 genomes]
rs9568066	0.81[ASN][1000 genomes]
rs9568067	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9568068	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9568070	0.81[ASN][1000 genomes]
rs9568071	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9568072	0.81[ASN][1000 genomes]
rs9568075	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9568077	0.92[ASN][1000 genomes]
rs9568079	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9634815	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9634816	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9634817	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9742182	0.83[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
rs1359107	ITM2B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:49228200-49234200	Weak transcription	GM12878-XiMat	blood
2	chr13:49229000-49234600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr13:49229000-49236800	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr13:49229600-49232600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr13:49229600-49234600	Weak transcription	Primary T cells from cord blood	blood
6	chr13:49229600-49235000	Weak transcription	Gastric	stomach
7	chr13:49229800-49234600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr13:49229800-49239400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr13:49230000-49232600	Weak transcription	Right Atrium	heart
10	chr13:49230000-49234200	Weak transcription	Primary hematopoietic stem cells	blood
11	chr13:49230000-49234400	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr13:49230000-49234400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr13:49231200-49234200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr13:49231200-49234200	Weak transcription	Adipose Nuclei	Adipose
15	chr13:49231200-49234200	Weak transcription	Fetal Lung	lung
16	chr13:49231200-49234400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr13:49231200-49234400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr13:49231400-49232600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr13:49231400-49232600	Weak transcription	Monocytes-CD14+_RO01746	blood
20	chr13:49231400-49233400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr13:49231400-49234200	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr13:49231400-49234200	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr13:49231400-49234200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr13:49231400-49234200	Weak transcription	Colon Smooth Muscle	Colon
25	chr13:49231400-49235000	Enhancers	Dnd41	blood
26	chr13:49231600-49234000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr13:49232200-49235600	Enhancers	Placenta	Placenta

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