Variant report

Variant	rs2583238
Chromosome Location	chr12:104277182-104277183
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10745981	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10745985	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861111	1.00[ASN][1000 genomes]
rs1165595	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1165667	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1165671	0.89[CEU][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1165679	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1165683	0.87[AFR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12809773	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	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2576953	1.00[ASN][1000 genomes]
rs2576956	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2576959	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2576968	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2576971	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2576976	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2722172	0.91[EUR][1000 genomes]
rs2919806	1.00[AFR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34309392	1.00[ASN][1000 genomes]
rs34811234	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]
rs71466284	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71466286	1.00[ASN][1000 genomes]
rs71466293	1.00[ASN][1000 genomes]
rs73175816	1.00[ASN][1000 genomes]
rs9669259	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9669708	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][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	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
3	nsv977145	chr12:104273790-104283207	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2583238	MIR3652	cis	Artery Tibial	GTEx
rs2583238	MIR3652	cis	Adipose Subcutaneous	GTEx
rs2583238	MIR3652	cis	Esophagus Mucosa	GTEx
rs2583238	MIR3652	cis	Esophagus Muscularis	GTEx
rs2583238	MIR3652	cis	Muscle Skeletal	GTEx
rs2583238	MIR3652	cis	Thyroid	GTEx
rs2583238	MIR3652	cis	Stomach	GTEx

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104254800-104278200	Weak transcription	Aorta	Aorta
2	chr12:104272200-104278200	Weak transcription	Primary T helper cells PMA-I stimulated	--
3	chr12:104273200-104277400	Enhancers	HMEC	breast
4	chr12:104273400-104277200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr12:104273400-104277600	Enhancers	NHEK	skin
6	chr12:104273800-104277200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr12:104274000-104277400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr12:104274400-104278000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr12:104275000-104281600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr12:104275600-104278200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr12:104275600-104278200	Weak transcription	Fetal Thymus	thymus
12	chr12:104275800-104277400	Weak transcription	Primary hematopoietic stem cells	blood
13	chr12:104276200-104277200	Enhancers	A549	lung
14	chr12:104276600-104277800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr12:104276800-104277200	Enhancers	Primary neutrophils fromperipheralblood	blood
16	chr12:104276800-104277200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
17	chr12:104276800-104278800	Enhancers	GM12878-XiMat	blood
18	chr12:104277000-104277200	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr12:104277000-104277200	Enhancers	Primary hematopoietic stem cells short term culture	blood

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