Variant report

Variant	rs9596215
Chromosome Location	chr13:50527565-50527566
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SPRYD7-1	chr13:50526411-50531031	NONHSAT033771

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1326120	0.86[AMR][1000 genomes]
rs2066549	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2066557	0.81[ASN][1000 genomes]
rs2066558	0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2066572	0.91[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2066575	0.92[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2066585	0.89[AMR][1000 genomes]
rs2066587	0.88[AMR][1000 genomes]
rs2066594	0.89[AMR][1000 genomes]
rs2242482	0.92[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2475837	0.81[ASN][1000 genomes]
rs2687951	0.89[AMR][1000 genomes]
rs2740508	0.89[AMR][1000 genomes]
rs2740524	0.82[ASN][1000 genomes]
rs2740544	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2740545	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2760914	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2803839	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2812204	0.83[AMR][1000 genomes]
rs2812216	0.88[AMR][1000 genomes]
rs2812217	0.88[AMR][1000 genomes]
rs2812222	0.89[AMR][1000 genomes]
rs2997624	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4548769	0.90[ASN][1000 genomes]
rs4942899	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4942901	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7336058	0.90[ASN][1000 genomes]
rs7338055	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9535407	0.91[ASN][1000 genomes]
rs9568354	0.91[ASN][1000 genomes]
rs9568363	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9568364	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9596219	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9596220	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[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	esv1834429	chr13:50509784-50536186	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	esv1837591	chr13:50513148-50530603	Weak transcription Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	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
4	nsv561630	chr13:50525141-50545402	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9596215	DLEU2///DLEU2L	trans	lymphoblastoid	RTeQTL
rs9596215	DLEU2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50511400-50537800	Weak transcription	Left Ventricle	heart
2	chr13:50513400-50532600	Weak transcription	Ovary	ovary
3	chr13:50513400-50532800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr13:50522400-50550600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr13:50525000-50530000	Enhancers	Placenta	Placenta
6	chr13:50525800-50532600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr13:50526200-50530000	Enhancers	Rectal Mucosa Donor 31	rectum
8	chr13:50526600-50527800	Weak transcription	Fetal Intestine Large	intestine
9	chr13:50526600-50528600	Weak transcription	Fetal Intestine Small	intestine
10	chr13:50526600-50529000	Weak transcription	HepG2	liver
11	chr13:50527000-50528600	Weak transcription	Rectal Mucosa Donor 29	rectum

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