Variant report

Variant	rs12091025
Chromosome Location	chr1:149989803-149989804
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	chr1:149853005..149861438-chr1:149978765..149991065,34	MCF-7	breast:
2	chr1:149906356..149909616-chr1:149987905..149990846,3	MCF-7	breast:
3	chr1:149855162..149857708-chr1:149989718..149991505,2	K562	blood:
4	chr1:149988147..149991518-chr1:149991864..149994674,3	K562	blood:
5	chr1:149988828..149991415-chr1:150020920..150022808,2	MCF-7	breast:
6	chr1:149864943..149867381-chr1:149988938..149991665,2	MCF-7	breast:
7	chr1:149856208..149858828-chr1:149989567..149991505,2	K562	blood:
8	chr1:149989681..149992599-chr1:150007188..150008846,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000184260	Chromatin interaction
ENSG00000014914	Chromatin interaction
ENSG00000184678	Chromatin interaction
ENSG00000178096	Chromatin interaction
ENSG00000184270	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10494259	1.00[ASW][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];0.90[YRI][hapmap];1.00[AMR][1000 genomes]
rs10494261	0.92[ASW][hapmap];0.88[MKK][hapmap]
rs1061955	1.00[AMR][1000 genomes]
rs11205308	0.92[ASW][hapmap];0.91[MKK][hapmap]
rs11205313	0.90[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11205314	1.00[AMR][1000 genomes]
rs12022928	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs12060171	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12060830	1.00[ASW][hapmap];0.94[LWK][hapmap];0.97[MKK][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes]
rs12064434	0.90[YRI][hapmap];1.00[AMR][1000 genomes]
rs12082035	1.00[ASW][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];0.90[YRI][hapmap];1.00[AMR][1000 genomes]
rs12091858	0.95[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12091904	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16833063	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16833149	1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs16833175	1.00[ASW][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16833178	0.92[ASW][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16838432	1.00[ASW][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];0.90[YRI][hapmap];1.00[AMR][1000 genomes]
rs4279885	0.90[YRI][hapmap];1.00[AMR][1000 genomes]
rs58342123	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59054339	0.89[AFR][1000 genomes]
rs74126211	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7517085	1.00[AMR][1000 genomes]
rs9804143	0.85[ASW][hapmap];0.86[MKK][hapmap];0.90[YRI][hapmap];1.00[AMR][1000 genomes]
rs9988489	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831537	chr1:149833357-150064655	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	431 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12091025	IFI44L	trans	brain	seeQTL
rs12091025	IFI44	trans	brain	seeQTL
rs12091025	OAS3	trans	brain	seeQTL

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:149982800-149994400	Weak transcription	Gastric	stomach
2	chr1:149983000-149992800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr1:149985000-149993200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr1:149985200-149993200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr1:149985400-149990200	Weak transcription	Brain Anterior Caudate	brain
6	chr1:149985400-149993000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr1:149985600-149994000	Weak transcription	Brain Hippocampus Middle	brain
8	chr1:149985600-150022000	Weak transcription	Brain Substantia Nigra	brain
9	chr1:149986200-149990400	Enhancers	Placenta	Placenta
10	chr1:149988000-149993200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr1:149988200-149992800	Weak transcription	Adipose Nuclei	Adipose
12	chr1:149988200-149992800	Weak transcription	A549	lung
13	chr1:149988200-149993200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr1:149988200-149993200	Weak transcription	Osteobl	bone
15	chr1:149988400-149993200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr1:149988800-149990000	Enhancers	Rectal Mucosa Donor 31	rectum
17	chr1:149988800-149991000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr1:149989000-149990000	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr1:149989000-149990000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr1:149989000-149990600	Enhancers	Stomach Mucosa	stomach
21	chr1:149989000-149991000	Enhancers	Fetal Intestine Small	intestine
22	chr1:149989200-149990000	Enhancers	HUES6 Cell Line	embryonic stem cell
23	chr1:149989200-149990400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
24	chr1:149989200-149990800	Enhancers	HUES64 Cell Line	embryonic stem cell
25	chr1:149989400-149990000	Enhancers	Fetal Intestine Large	intestine
26	chr1:149989400-149990000	Enhancers	Skeletal Muscle Female	skeletal muscle
27	chr1:149989400-149990000	Enhancers	Hela-S3	cervix
28	chr1:149989400-149991200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr1:149989600-149990000	Enhancers	Colonic Mucosa	Colon
30	chr1:149989600-149990600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr1:149989600-149990600	Enhancers	Rectal Mucosa Donor 29	rectum
32	chr1:149989600-149993200	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr1:149989600-149993200	Weak transcription	K562	blood
34	chr1:149989600-149997800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr1:149989600-149998000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr1:149989800-149990600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
37	chr1:149989800-149990800	Flanking Active TSS	GM12878-XiMat	blood
38	chr1:149989800-149992000	Weak transcription	Pancreas	Pancrea
39	chr1:149989800-149993200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr1:149989800-149993200	Weak transcription	NHEK	skin
41	chr1:149989800-149993400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr1:149989800-149993400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr1:149989800-149993400	Weak transcription	HMEC	breast
44	chr1:149989800-149993600	Weak transcription	HUES48 Cell Line	embryonic stem cell

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