Variant report

Variant	rs9669708
Chromosome Location	chr12:104262070-104262071
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:104163986..104166339-chr12:104260477..104262512,3	MCF-7	breast:
2	chr12:104233414..104235645-chr12:104261719..104263696,2	MCF-7	breast:
3	chr12:104234662..104237324-chr12:104259230..104262191,2	MCF-7	breast:
4	chr12:104229521..104231135-chr12:104260816..104262846,2	K562	blood:
5	chr12:104257250..104260227-chr12:104261729..104263369,2	K562	blood:

Variant related genes	Relation type
ENSG00000111696	Chromatin interaction
ENSG00000257327	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10745981	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10745985	1.00[ASW][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861111	1.00[ASN][1000 genomes]
rs11111768	1.00[JPT][hapmap]
rs11612613	1.00[LWK][hapmap];0.91[MKK][hapmap]
rs1165595	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1165667	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1165671	0.89[CEU][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1165679	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1165683	0.87[AFR][1000 genomes];0.82[EUR][1000 genomes];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];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1992208	0.83[TSI][hapmap]
rs2255584	0.83[TSI][hapmap]
rs2255791	0.83[TSI][hapmap]
rs2255794	0.83[TSI][hapmap]
rs2255795	0.83[TSI][hapmap]
rs2255797	0.83[TSI][hapmap]
rs2438111	0.83[TSI][hapmap]
rs2576953	1.00[ASN][1000 genomes]
rs2576956	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2576959	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2576968	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2576971	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2576976	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2583238	1.00[CEU][hapmap]
rs2722172	0.88[EUR][1000 genomes]
rs2919806	1.00[AFR][1000 genomes];0.95[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]
rs6539095	1.00[ASW][hapmap]
rs71466284	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71466286	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];1.00[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:12)

SNP	Gene	Cis/trans	Tissue	Source
rs9669708	MIR3652	cis	Adipose Subcutaneous	GTEx
rs9669708	ALDH1L2	cis	parietal	SCAN
rs9669708	MIR3652	cis	Stomach	GTEx
rs9669708	MIR3652	cis	Thyroid	GTEx
rs9669708	GLT8D2	cis	parietal	SCAN
rs9669708	MIR3652	cis	Esophagus Mucosa	GTEx
rs9669708	SLC41A2	cis	parietal	SCAN
rs9669708	MIR3652	cis	Artery Tibial	GTEx
rs9669708	MIR3652	cis	Muscle Skeletal	GTEx
rs9669708	NT5DC3	cis	parietal	SCAN
rs9669708	VSTM2B	trans	cerebellum	SCAN
rs9669708	MIR3652	cis	Esophagus Muscularis	GTEx

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104250000-104263800	Weak transcription	Liver	Liver
2	chr12:104254800-104278200	Weak transcription	Aorta	Aorta
3	chr12:104255600-104262200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr12:104259200-104262400	Weak transcription	HSMM	muscle
5	chr12:104259200-104263800	Weak transcription	HepG2	liver
6	chr12:104260200-104262800	Enhancers	Colon Smooth Muscle	Colon
7	chr12:104261400-104262800	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr12:104261600-104263200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr12:104261800-104262800	Enhancers	Rectal Smooth Muscle	rectum
10	chr12:104262000-104262200	Enhancers	Pancreatic Islets	Pancreatic Islet
11	chr12:104262000-104262800	Enhancers	Muscle Satellite Cultured Cells	--
12	chr12:104262000-104262800	Enhancers	HSMMtube	muscle

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