Variant report

Variant	rs26953
Chromosome Location	chr5:59814314-59814315
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs152324	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs153153	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs206789	0.87[ASW][hapmap];0.84[MEX][hapmap]
rs26949	0.88[ASN][1000 genomes]
rs26950	0.90[ASN][1000 genomes]
rs26954	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs286158	0.87[ASW][hapmap];0.84[MEX][hapmap]
rs35382	0.90[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs35383	0.95[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35384	0.95[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4515250	0.87[ASW][hapmap]
rs4699958	0.86[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	nsv1025856	chr5:59188419-59928852	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv598288	chr5:59627555-60003460	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv1018614	chr5:59708223-59910308	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv881711	chr5:59724947-59890278	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv598297	chr5:59734004-59862453	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs26953	DEPDC1B	Cis_1M	lymphoblastoid	RTeQTL
rs26953	ELOVL7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:59804200-59815800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr5:59806800-59816000	Weak transcription	Fetal Muscle Leg	muscle
3	chr5:59810600-59816000	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr5:59812400-59816000	Weak transcription	Right Atrium	heart
5	chr5:59812800-59814400	Weak transcription	Primary B cells from cord blood	blood
6	chr5:59812800-59814600	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr5:59812800-59816800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr5:59812800-59822400	Weak transcription	Brain Angular Gyrus	brain
9	chr5:59813000-59814400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr5:59813200-59814600	Weak transcription	Fetal Stomach	stomach
11	chr5:59813600-59815200	Flanking Active TSS	Stomach Smooth Muscle	stomach
12	chr5:59813600-59816200	Weak transcription	Placenta	Placenta
13	chr5:59813800-59815600	Flanking Active TSS	GM12878-XiMat	blood
14	chr5:59813800-59817600	Enhancers	Rectal Smooth Muscle	rectum
15	chr5:59814000-59814400	Weak transcription	Primary B cells from peripheral blood	blood
16	chr5:59814000-59816200	Weak transcription	Spleen	Spleen
17	chr5:59814000-59819600	Enhancers	Colon Smooth Muscle	Colon
18	chr5:59814200-59814800	Weak transcription	Right Ventricle	heart
19	chr5:59814200-59815200	Weak transcription	Brain Hippocampus Middle	brain
20	chr5:59814200-59816000	Weak transcription	Gastric	stomach
21	chr5:59814200-59816000	Weak transcription	Left Ventricle	heart
22	chr5:59814200-59816000	Weak transcription	Pancreas	Pancrea
23	chr5:59814200-59817600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links