Variant report

Variant	rs469702
Chromosome Location	chr5:112293523-112293524
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:112256942..112259777-chr5:112292490..112295980,4	MCF-7	breast:
2	chr5:112256312..112258572-chr5:112293343..112296094,6	MCF-7	breast:
3	chr5:112252458..112254818-chr5:112292295..112294312,2	K562	blood:
4	chr5:112293295..112296045-chr5:112298149..112301329,3	MCF-7	breast:
5	chr5:112292348..112294065-chr5:112295595..112297511,2	MCF-7	breast:
6	chr5:112291720..112294004-chr5:112309905..112311791,2	MCF-7	breast:
7	chr5:112292808..112297954-chr5:112311731..112314309,4	MCF-7	breast:
8	chr5:112292660..112295480-chr5:112309614..112313888,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000172795	Chromatin interaction
ENSG00000129625	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs149502	0.88[EUR][1000 genomes]
rs153562	0.82[EUR][1000 genomes]
rs153566	0.91[EUR][1000 genomes]
rs153568	0.95[EUR][1000 genomes]
rs153570	0.97[EUR][1000 genomes]
rs153571	0.90[EUR][1000 genomes]
rs1625623	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs173466	0.81[EUR][1000 genomes]
rs469523	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs469675	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs469716	0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029271	chr5:112113308-112325943	Strong transcription Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv599394	chr5:112185491-112446323	Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv1019756	chr5:112242315-112325943	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs469702	SRP19	Cis_1M	lymphoblastoid	RTeQTL
rs469702	REEP5	cis	Esophagus Muscularis	GTEx

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112291600-112297600	Enhancers	HepG2	liver
2	chr5:112291800-112294400	Enhancers	Brain Germinal Matrix	brain
3	chr5:112292200-112294400	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr5:112292600-112293800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr5:112292600-112294200	Flanking Active TSS	A549	lung
6	chr5:112292600-112295000	Enhancers	Hela-S3	cervix
7	chr5:112292600-112295200	Weak transcription	Fetal Muscle Trunk	muscle
8	chr5:112292800-112293800	Enhancers	Muscle Satellite Cultured Cells	--
9	chr5:112292800-112293800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr5:112292800-112294800	Enhancers	Fetal Brain Female	brain
11	chr5:112292800-112295200	Enhancers	Adipose Nuclei	Adipose
12	chr5:112292800-112295600	Weak transcription	Lung	lung
13	chr5:112293000-112294000	Enhancers	NH-A	brain
14	chr5:112293000-112294400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr5:112293000-112295200	Enhancers	Liver	Liver
16	chr5:112293200-112293600	Weak transcription	Fetal Lung	lung
17	chr5:112293200-112293800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr5:112293200-112294200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr5:112293200-112294200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
20	chr5:112293200-112294400	Enhancers	Fetal Brain Male	brain
21	chr5:112293200-112294600	Enhancers	Osteobl	bone
22	chr5:112293200-112294800	Enhancers	Brain Angular Gyrus	brain
23	chr5:112293200-112295000	Enhancers	HUES48 Cell Line	embryonic stem cell
24	chr5:112293200-112295200	Enhancers	HUES64 Cell Line	embryonic stem cell
25	chr5:112293200-112296400	Enhancers	Stomach Smooth Muscle	stomach
26	chr5:112293200-112296400	Enhancers	HSMMtube	muscle
27	chr5:112293200-112296400	Enhancers	HUVEC	blood vessel
28	chr5:112293200-112297000	Enhancers	NHDF-Ad	bronchial
29	chr5:112293200-112297000	Enhancers	NHLF	lung
30	chr5:112293400-112294000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr5:112293400-112297200	Enhancers	Fetal Muscle Leg	muscle
32	chr5:112293400-112297200	Enhancers	Fetal Stomach	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links