Variant report

Variant	rs11183699
Chromosome Location	chr12:47426533-47426534
allele	A/G
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:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:47426131..47426995-chr12:47801759..47802680,2	MCF-7	breast:
2	chr12:47426514..47428986-chr12:47432819..47435080,2	K562	blood:
3	chr12:47426173..47426997-chr12:47791154..47791760,2	MCF-7	breast:
4	chr12:47424729..47426911-chr12:47456860..47459530,2	MCF-7	breast:
5	chr12:47423549..47426668-chr12:47427215..47430937,3	K562	blood:
6	chr12:47424715..47431022-chr12:47469878..47476557,9	MCF-7	breast:
7	chr12:47426143..47427022-chr12:47801754..47802533,5	MCF-7	breast:
8	chr12:47426139..47426692-chr12:47701630..47702130,2	MCF-7	breast:
9	chr12:47426451..47427271-chr12:47464647..47465666,4	MCF-7	breast:
10	chr12:47425063..47426627-chr12:47473184..47475251,2	MCF-7	breast:
11	chr12:47426141..47427023-chr12:47464823..47465697,2	MCF-7	breast:
12	chr12:47426505..47427015-chr12:48080605..48081500,2	K562	blood:
13	chr12:47426075..47427622-chr12:47476295..47478155,2	MCF-7	breast:
14	chr12:47426174..47426833-chr12:48051074..48051739,2	MCF-7	breast:
15	chr12:47426078..47427592-chr12:47799821..47802354,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000139211	Chromatin interaction
ENSG00000179715	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10785651	0.95[ASN][1000 genomes]
rs10881025	0.80[AMR][1000 genomes]
rs10881039	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11183677	0.88[EUR][1000 genomes]
rs11183695	0.85[AMR][1000 genomes]
rs11183706	0.95[ASN][1000 genomes]
rs11183710	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11183711	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1989912	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2263492	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2408647	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2522258	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2522269	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2522275	0.80[AMR][1000 genomes]
rs2711702	0.82[AMR][1000 genomes]
rs34142537	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4768770	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7134654	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7139072	0.82[AMR][1000 genomes]
rs7305283	0.82[AMR][1000 genomes]
rs7305847	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7956438	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7958568	0.96[CEU][hapmap];0.89[GIH][hapmap];0.93[TSI][hapmap];0.96[EUR][1000 genomes]
rs7960974	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7971310	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7971796	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7972871	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7978950	0.86[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	esv1845143	chr12:47051076-47431496	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv469368	chr12:47374908-47675680	Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv558784	chr12:47374908-47675680	Genic enhancers Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11183699	PFKM	cis	cerebellum	SCAN
rs11183699	RAPGEF3	cis	cerebellum	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:47418000-47428400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:47418400-47426600	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr12:47419200-47426600	Weak transcription	Osteobl	bone
4	chr12:47423600-47426600	Weak transcription	Hela-S3	cervix
5	chr12:47423800-47426600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr12:47426000-47426600	Enhancers	A549	lung
7	chr12:47426200-47427000	Weak transcription	Fetal Intestine Large	intestine
8	chr12:47426200-47427200	Enhancers	Primary T cells from cord blood	blood
9	chr12:47426200-47428800	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr12:47426400-47426600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr12:47426400-47428200	Enhancers	Primary T helper cells fromperipheralblood	blood

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