Variant report

Variant	rs9596240
Chromosome Location	chr13:50731779-50731780
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:50727152..50729552-chr13:50729761..50732291,3	MCF-7	breast:
2	chr13:50724073..50728700-chr13:50729258..50733237,4	K562	blood:
3	chr13:50563719..50566277-chr13:50730745..50733012,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RNASEH2B-3	chr13:50730963-50732212	NONHSAT033821

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs12100048	0.86[EUR][1000 genomes]
rs1323451	0.86[EUR][1000 genomes]
rs17073724	0.86[EUR][1000 genomes]
rs17073826	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17073834	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17471092	0.96[EUR][1000 genomes]
rs1963729	0.82[EUR][1000 genomes]
rs2066566	0.81[EUR][1000 genomes]
rs2066586	0.84[EUR][1000 genomes]
rs2066598	0.85[EUR][1000 genomes]
rs61961304	0.82[EUR][1000 genomes]
rs61961305	0.82[EUR][1000 genomes]
rs61961323	0.82[EUR][1000 genomes]
rs61961325	0.82[EUR][1000 genomes]
rs61961327	0.86[EUR][1000 genomes]
rs61961328	0.86[EUR][1000 genomes]
rs61962359	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6561575	0.85[EUR][1000 genomes]
rs73196768	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7325091	0.84[EUR][1000 genomes]
rs7325993	0.86[EUR][1000 genomes]
rs7981648	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7991744	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1035151	chr13:50513535-51167850	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1254 gene(s)	inside rSNPs	diseases
2	esv2753964	chr13:50545399-51421199	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Genic enhancers Strong transcription 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	1256 gene(s)	inside rSNPs	diseases
3	esv2753492	chr13:50550081-51461720	Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1256 gene(s)	inside rSNPs	diseases
4	esv2752608	chr13:50550099-51054499	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1249 gene(s)	inside rSNPs	diseases
5	nsv832608	chr13:50678628-50888413	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
6	nsv1041501	chr13:50683189-50795195	Flanking Active TSS Weak transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
7	nsv900076	chr13:50710579-50912578	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9596240	DLEU1	Cis_1M	lymphoblastoid	RTeQTL
rs9596240	TRIM13	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50724400-50733400	Weak transcription	Psoas Muscle	Psoas
2	chr13:50726800-50734600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr13:50726800-50735000	Weak transcription	NHLF	lung
4	chr13:50727000-50732400	Weak transcription	Primary B cells from cord blood	blood
5	chr13:50728000-50732600	Weak transcription	Primary B cells from peripheral blood	blood
6	chr13:50728800-50733400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr13:50729000-50731800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr13:50730000-50732000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr13:50730800-50734800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr13:50731200-50734400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr13:50731200-50735000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr13:50731200-50735200	Weak transcription	Osteobl	bone
13	chr13:50731400-50734600	Weak transcription	NHDF-Ad	bronchial
14	chr13:50731400-50736200	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr13:50731400-50736600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr13:50731600-50733200	Weak transcription	HepG2	liver
17	chr13:50731600-50735000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links