Variant report

Variant	rs11183666
Chromosome Location	chr12:47335529-47335530
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10785646	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10881009	0.86[EUR][1000 genomes]
rs10881011	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10881013	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11183625	0.80[CHB][hapmap]
rs11183661	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11183665	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11183671	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11183672	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11609950	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12229470	0.85[EUR][1000 genomes]
rs12423364	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1986584	0.86[EUR][1000 genomes]
rs2250595	0.80[EUR][1000 genomes]
rs2253630	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2465221	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2465222	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2465223	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2465227	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2465228	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2465229	0.83[EUR][1000 genomes]
rs2465230	0.95[MEX][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs2465232	0.83[EUR][1000 genomes]
rs2465597	0.83[EUR][1000 genomes]
rs2465617	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2465627	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2465628	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2465630	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4374015	0.80[CHB][hapmap]
rs4405401	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4586261	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6582686	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7137808	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7138703	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7295618	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7962539	0.81[EUR][1000 genomes]
rs7963326	0.86[EUR][1000 genomes]
rs7966987	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7975211	0.90[EUR][1000 genomes];0.94[ASN][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	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11183666	RAPGEF3	cis	cerebellum	SCAN
rs11183666	PFKM	cis	cerebellum	SCAN
rs11183666	CCNT1	cis	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:47332400-47335600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr12:47332400-47335600	Weak transcription	HMEC	breast
3	chr12:47332400-47335800	Weak transcription	Osteobl	bone
4	chr12:47332400-47336200	Weak transcription	NH-A	brain
5	chr12:47332400-47337600	Weak transcription	A549	lung
6	chr12:47332600-47335600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr12:47332600-47335800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr12:47332600-47336000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr12:47332800-47335600	Weak transcription	NHEK	skin
10	chr12:47332800-47336600	Weak transcription	Liver	Liver
11	chr12:47332800-47338000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr12:47333000-47335800	Weak transcription	NHLF	lung
13	chr12:47335400-47338800	Enhancers	HSMM	muscle
14	chr12:47335400-47339000	Enhancers	Muscle Satellite Cultured Cells	--

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