Variant report

Variant	rs28368295
Chromosome Location	chr3:191132640-191132641
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs13326246	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13434281	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17545865	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17754685	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17811727	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2164237	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28448537	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28502671	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28510847	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4677634	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4687210	0.86[EUR][1000 genomes]
rs9290985	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs980320	0.94[EUR][1000 genomes]
rs980321	0.94[EUR][1000 genomes]
rs9825936	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9826141	0.94[EUR][1000 genomes]
rs9827142	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9839989	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9844109	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9844500	0.82[AFR][1000 genomes]
rs9854318	0.82[AFR][1000 genomes]
rs9854581	0.82[AFR][1000 genomes]
rs9855282	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9868286	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9868495	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931943	chr3:190860224-191321873	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	esv2757910	chr3:190867011-191279107	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	esv2759209	chr3:190867011-191279107	Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv428428	chr3:190936834-191215596	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv998208	chr3:191021434-191175350	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv534269	chr3:191037181-191261730	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs28368295	CCDC50	cis	Esophagus Muscularis	GTEx
rs28368295	CCDC50	cis	Nerve Tibial	GTEx
rs28368295	CCDC50	cis	Artery Tibial	GTEx
rs28368295	CCDC50	cis	Thyroid	GTEx

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:191129000-191134600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:191129400-191135200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr3:191130200-191132800	Enhancers	NHDF-Ad	bronchial
4	chr3:191130600-191132800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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