Variant report

Variant	rs71466284
Chromosome Location	chr12:104258076-104258077
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:104252726..104255857-chr12:104256920..104259686,3	MCF-7	breast:
2	chr12:104257250..104260227-chr12:104261729..104263369,2	K562	blood:
3	chr12:104256917..104259122-chr12:104264989..104267074,2	MCF-7	breast:
4	chr12:104233269..104235056-chr12:104256558..104259181,2	K562	blood:

Variant related genes	Relation type
ENSG00000111696	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10745981	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10745985	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861111	1.00[ASN][1000 genomes]
rs1165595	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1165667	0.86[AFR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1165671	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1165679	0.86[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1165683	1.00[ASN][1000 genomes]
rs12813601	1.00[ASN][1000 genomes]
rs12819539	1.00[ASN][1000 genomes]
rs12823195	1.00[ASN][1000 genomes]
rs17034955	1.00[ASN][1000 genomes]
rs1866075	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2576953	1.00[ASN][1000 genomes]
rs2576956	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2576959	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2576968	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2576971	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2576976	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2722172	0.86[EUR][1000 genomes]
rs2919806	0.86[AFR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34309392	1.00[ASN][1000 genomes]
rs34863477	1.00[ASN][1000 genomes]
rs35392305	1.00[ASN][1000 genomes]
rs35642814	1.00[ASN][1000 genomes]
rs35844634	1.00[ASN][1000 genomes]
rs4964197	1.00[ASN][1000 genomes]
rs57749959	1.00[ASN][1000 genomes]
rs61939568	1.00[ASN][1000 genomes]
rs71466286	1.00[ASN][1000 genomes]
rs73175816	1.00[ASN][1000 genomes]
rs9669259	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9669708	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34031	chr12:104114277-104298546	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
2	nsv560039	chr12:104177668-104455340	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs71466284	MIR3652	cis	Thyroid	GTEx
rs71466284	MIR3652	cis	Artery Tibial	GTEx
rs71466284	MIR3652	cis	Esophagus Muscularis	GTEx
rs71466284	MIR3652	cis	Stomach	GTEx
rs71466284	MIR3652	cis	Esophagus Mucosa	GTEx

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104250000-104263800	Weak transcription	Liver	Liver
2	chr12:104253600-104261600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr12:104254000-104258600	Weak transcription	HSMMtube	muscle
4	chr12:104254400-104258600	Weak transcription	HSMM	muscle
5	chr12:104254400-104258800	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr12:104254800-104278200	Weak transcription	Aorta	Aorta
7	chr12:104255000-104259200	Weak transcription	Osteobl	bone
8	chr12:104255600-104262200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr12:104256800-104258200	Enhancers	Stomach Smooth Muscle	stomach
10	chr12:104257000-104259200	Enhancers	HepG2	liver
11	chr12:104257200-104259200	Enhancers	Placenta	Placenta
12	chr12:104257600-104259200	Enhancers	Esophagus	oesophagus
13	chr12:104257800-104258600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr12:104257800-104259200	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr12:104257800-104259200	Enhancers	Colon Smooth Muscle	Colon
16	chr12:104257800-104259200	Enhancers	Fetal Thymus	thymus
17	chr12:104257800-104260200	Enhancers	HMEC	breast
18	chr12:104257800-104260400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr12:104258000-104259800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr12:104258000-104260200	Enhancers	NHEK	skin
21	chr12:104258000-104261800	Weak transcription	Rectal Smooth Muscle	rectum

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