Variant report

Variant	rs2465223
Chromosome Location	chr12:47336910-47336911
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10785646	0.85[EUR][1000 genomes]
rs10881011	0.83[EUR][1000 genomes]
rs10881013	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs11183661	0.81[CEU][hapmap]
rs11183665	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11183666	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11183671	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11183672	0.85[EUR][1000 genomes]
rs11609950	0.83[EUR][1000 genomes]
rs12423364	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2465221	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2465222	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2465227	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2465228	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2465229	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2465230	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2465232	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2465597	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2465617	0.95[EUR][1000 genomes]
rs4586261	0.86[EUR][1000 genomes]
rs6582686	0.80[EUR][1000 genomes]
rs7138703	0.86[EUR][1000 genomes]
rs7295618	0.80[EUR][1000 genomes]
rs7966987	0.83[EUR][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2465223	CCNT1	cis	parietal	SCAN
rs2465223	PFKM	cis	cerebellum	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:47332400-47337600	Weak transcription	A549	lung
2	chr12:47332800-47338000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr12:47335400-47338800	Enhancers	HSMM	muscle
4	chr12:47335400-47339000	Enhancers	Muscle Satellite Cultured Cells	--
5	chr12:47335600-47337200	Enhancers	Hela-S3	cervix
6	chr12:47335600-47337400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr12:47335600-47337400	Enhancers	HMEC	breast
8	chr12:47335600-47337600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr12:47335600-47338400	Enhancers	Skeletal Muscle Male	skeletal muscle
10	chr12:47335600-47338400	Enhancers	NHEK	skin
11	chr12:47335800-47337000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr12:47335800-47337000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr12:47335800-47337000	Enhancers	Psoas Muscle	Psoas
14	chr12:47335800-47337200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr12:47335800-47337200	Enhancers	HUVEC	blood vessel
16	chr12:47335800-47338200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr12:47335800-47338200	Enhancers	Osteobl	bone
18	chr12:47335800-47339400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr12:47335800-47343400	Enhancers	NHDF-Ad	bronchial
20	chr12:47336000-47338400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr12:47336200-47337200	Enhancers	NH-A	brain
22	chr12:47336400-47338800	Enhancers	Skeletal Muscle Female	skeletal muscle
23	chr12:47336600-47337000	Enhancers	Fetal Heart	heart
24	chr12:47336600-47337200	Enhancers	Liver	Liver
25	chr12:47336600-47338400	Enhancers	HSMMtube	muscle
26	chr12:47336800-47337200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr12:47336800-47337600	Enhancers	NHLF	lung

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