Variant report

Variant	rs1005409
Chromosome Location	chr20:25044023-25044024
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:25043693..25045702-chr20:25047001..25049231,2	MCF-7	breast:
2	chr20:24959138..24961345-chr20:25043562..25046337,2	MCF-7	breast:
3	chr20:24975304..24980368-chr20:25042845..25047055,6	MCF-7	breast:

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs12480307	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2207632	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2207633	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2207635	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2207636	1.00[ASN][1000 genomes]
rs2387577	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4813546	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4813548	1.00[ASN][1000 genomes]
rs4815365	0.88[EUR][1000 genomes]
rs4815366	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4815367	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4815368	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55651034	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56157240	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56369722	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58747756	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6037014	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050299	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050300	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050304	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050306	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050308	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6076315	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6083734	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6083736	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083737	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083739	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083745	0.84[ASN][1000 genomes]
rs6115024	1.00[ASN][1000 genomes]
rs6115037	1.00[ASN][1000 genomes]
rs61304082	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62215277	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62217194	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62217195	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62217196	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62217197	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62217199	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7263632	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7265950	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7266451	1.00[ASN][1000 genomes]
rs7344824	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs743017	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][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	nsv1062140	chr20:24807962-25304054	Strong transcription Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv544219	chr20:24807962-25304054	Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv1056345	chr20:24819570-25168159	Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv1055341	chr20:24848416-25302271	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv912826	chr20:24987787-25071454	Flanking Active TSS Genic enhancers Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1005409	ABHD12	Cis_1M	lymphoblastoid	RTeQTL
rs1005409	VSX1	cis	brain	BrainEAC

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25039600-25044600	Enhancers	Pancreas	Pancrea
2	chr20:25039600-25044800	Weak transcription	Brain Anterior Caudate	brain
3	chr20:25039600-25044800	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr20:25039800-25044800	Weak transcription	Right Ventricle	heart
5	chr20:25039800-25045400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr20:25040200-25045200	Weak transcription	Brain Hippocampus Middle	brain
7	chr20:25040200-25045200	Weak transcription	Left Ventricle	heart
8	chr20:25040200-25046000	Weak transcription	Spleen	Spleen
9	chr20:25040400-25045200	Weak transcription	Brain Cingulate Gyrus	brain
10	chr20:25040600-25045800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr20:25040800-25045600	Weak transcription	Dnd41	blood
12	chr20:25040800-25046200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr20:25041000-25046200	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr20:25042000-25045800	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr20:25042400-25044400	Enhancers	Primary B cells from peripheral blood	blood
16	chr20:25042600-25045600	Weak transcription	Liver	Liver
17	chr20:25042600-25045600	Bivalent Enhancer	HepG2	liver
18	chr20:25042800-25045200	Weak transcription	Stomach Mucosa	stomach
19	chr20:25042800-25045800	Weak transcription	Gastric	stomach
20	chr20:25043000-25045200	Weak transcription	Fetal Intestine Large	intestine
21	chr20:25043200-25044400	Enhancers	Fetal Thymus	thymus
22	chr20:25043200-25045400	Weak transcription	Fetal Intestine Small	intestine
23	chr20:25043800-25045600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links