Variant report

Variant	rs12091858
Chromosome Location	chr1:149988000-149988001
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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	chr1:149986387..149989368-chr1:150040476..150042209,2	MCF-7	breast:
4	chr1:149975951..149977687-chr1:149986866..149989017,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-VPS45-7	chr1:149987339-149988598	NONHSAT006262

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

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10494259	0.86[YRI][hapmap];1.00[AMR][1000 genomes]
rs1061955	1.00[AMR][1000 genomes]
rs11205313	0.82[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11205314	1.00[AMR][1000 genomes]
rs12022928	0.95[YRI][hapmap];0.84[AFR][1000 genomes]
rs12060171	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12060830	0.90[YRI][hapmap];0.87[AFR][1000 genomes]
rs12064434	0.86[YRI][hapmap];1.00[AMR][1000 genomes]
rs12082035	0.86[YRI][hapmap];1.00[AMR][1000 genomes]
rs12091025	0.95[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12091904	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16833063	0.95[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16833149	0.95[YRI][hapmap];0.93[AFR][1000 genomes]
rs16833175	0.90[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16833178	0.90[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16838432	0.86[YRI][hapmap];1.00[AMR][1000 genomes]
rs4279885	0.86[YRI][hapmap];1.00[AMR][1000 genomes]
rs58342123	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59054339	0.87[AFR][1000 genomes]
rs74126211	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7517085	1.00[AMR][1000 genomes]
rs9804143	0.86[YRI][hapmap];1.00[AMR][1000 genomes]
rs9988489	0.95[YRI][hapmap];0.83[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

No data

Chromatin state (count:37 , 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	chr1:149983400-149988800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr1:149983400-149988800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr1:149983400-149989000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr1:149983400-149989400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr1:149983400-149989400	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr1:149985000-149989400	Weak transcription	Hela-S3	cervix
9	chr1:149985000-149989600	Weak transcription	Colonic Mucosa	Colon
10	chr1:149985000-149993200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr1:149985200-149988800	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr1:149985200-149989000	Weak transcription	Stomach Mucosa	stomach
13	chr1:149985200-149989400	Weak transcription	GM12878-XiMat	blood
14	chr1:149985200-149993200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr1:149985400-149988800	Weak transcription	Fetal Intestine Large	intestine
16	chr1:149985400-149988800	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr1:149985400-149989600	Weak transcription	Brain Cingulate Gyrus	brain
18	chr1:149985400-149990200	Weak transcription	Brain Anterior Caudate	brain
19	chr1:149985400-149993000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr1:149985600-149989000	Weak transcription	Fetal Intestine Small	intestine
21	chr1:149985600-149994000	Weak transcription	Brain Hippocampus Middle	brain
22	chr1:149985600-150022000	Weak transcription	Brain Substantia Nigra	brain
23	chr1:149986200-149990400	Enhancers	Placenta	Placenta
24	chr1:149986600-149988200	Enhancers	K562	blood
25	chr1:149986800-149989000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr1:149987000-149988200	Enhancers	Adipose Nuclei	Adipose
27	chr1:149987400-149988000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr1:149987400-149989800	Enhancers	Placenta Amnion	Placenta Amnion
29	chr1:149987600-149988000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr1:149987600-149988000	Enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr1:149987600-149988200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr1:149987600-149988200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr1:149987600-149988200	Enhancers	A549	lung
34	chr1:149987600-149988200	Enhancers	Osteobl	bone
35	chr1:149987800-149988000	Weak transcription	Right Atrium	heart
36	chr1:149988000-149988400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr1:149988000-149993200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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