Variant report

Variant	rs60071944
Chromosome Location	chr3:100216169-100216170
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs11920006	0.96[ASN][1000 genomes]
rs11923942	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11926280	0.87[ASN][1000 genomes]
rs11927516	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12631075	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12634371	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12636805	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12639465	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4132537	0.87[ASN][1000 genomes]
rs4928097	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4928098	0.96[ASN][1000 genomes]
rs57018910	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs58059387	0.96[ASN][1000 genomes]
rs59299896	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59771628	0.96[ASN][1000 genomes]
rs60272820	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61636409	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62276517	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62276520	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62276521	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62276522	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62276523	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62276526	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62276527	0.87[ASN][1000 genomes]
rs62276556	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62276559	0.89[EUR][1000 genomes]
rs6441285	0.88[ASN][1000 genomes]
rs66791174	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs67600559	0.95[EUR][1000 genomes]
rs6763079	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6763178	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67774605	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6789867	0.96[ASN][1000 genomes]
rs6798264	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73152126	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7429072	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7429277	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7429604	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7430698	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7430715	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7431846	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7619507	0.95[ASN][1000 genomes]
rs7630198	0.96[ASN][1000 genomes]
rs9813069	0.83[ASN][1000 genomes]
rs9851429	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[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	nsv877218	chr3:100176360-100267619	Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs60071944	TMEM45A	cis	Whole Blood	GTEx

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:100212400-100219200	Weak transcription	Aorta	Aorta
2	chr3:100212400-100222800	Weak transcription	Ovary	ovary
3	chr3:100212800-100217800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr3:100212800-100224800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr3:100213200-100216400	Weak transcription	Fetal Stomach	stomach
6	chr3:100213400-100217600	Enhancers	Placenta Amnion	Placenta Amnion
7	chr3:100214000-100223600	Weak transcription	Fetal Lung	lung
8	chr3:100214400-100216400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr3:100214400-100216400	Enhancers	NHDF-Ad	bronchial
10	chr3:100214400-100217400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr3:100214600-100219400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr3:100214800-100216200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr3:100214800-100216200	Enhancers	HSMM	muscle
14	chr3:100214800-100216400	Enhancers	HMEC	breast
15	chr3:100214800-100216800	Enhancers	NHEK	skin
16	chr3:100215000-100216200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr3:100215000-100216400	Enhancers	Muscle Satellite Cultured Cells	--
18	chr3:100215200-100216200	Enhancers	HSMMtube	muscle
19	chr3:100215200-100216200	Enhancers	NHLF	lung
20	chr3:100215200-100216400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr3:100215200-100216400	Enhancers	NH-A	brain
22	chr3:100215400-100216200	Enhancers	Primary B cells from peripheral blood	blood
23	chr3:100215400-100216200	Enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr3:100215400-100216200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr3:100215400-100216400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr3:100215400-100218600	Weak transcription	Liver	Liver
27	chr3:100215600-100216200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr3:100215600-100217400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr3:100215800-100216200	Enhancers	Primary neutrophils fromperipheralblood	blood
30	chr3:100215800-100216400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr3:100215800-100219400	Weak transcription	Osteobl	bone
32	chr3:100216000-100216400	Enhancers	GM12878-XiMat	blood
33	chr3:100216000-100218600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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