Variant report

Variant	rs28728311
Chromosome Location	chr21:40863223-40863224
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11088478	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11702769	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12482418	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13050145	0.81[EUR][1000 genomes]
rs1474384	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1475593	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1524929	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2026268	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2837045	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2837046	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2837047	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2837048	0.84[AMR][1000 genomes]
rs2837049	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2837050	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2837053	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2837055	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs28634277	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3787927	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4818041	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6517553	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7277107	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7278885	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7280971	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7281076	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8126860	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8128567	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8128795	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9976202	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9976208	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9983297	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1059868	chr21:40711535-41043291	Active TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv1061454	chr21:40757973-41265404	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv1062088	chr21:40838027-40919253	Enhancers Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1067330	chr21:40841948-40879552	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	esv2755103	chr21:40847196-40877805	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	esv2756754	chr21:40857523-40966156	Enhancers Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	esv2758820	chr21:40857523-40966156	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv964496	chr21:40861855-40863688	Weak transcription Enhancers Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs28728311	LCA5L	cis	Thyroid	GTEx
rs28728311	SH3BGR	cis	Thyroid	GTEx
rs28728311	LCA5L	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40827400-40879800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr21:40836400-40894800	Weak transcription	Right Ventricle	heart
3	chr21:40848200-40895600	Weak transcription	Stomach Smooth Muscle	stomach
4	chr21:40848400-40863600	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr21:40848400-40872400	Weak transcription	Left Ventricle	heart
6	chr21:40852600-40863400	Weak transcription	Brain Cingulate Gyrus	brain
7	chr21:40853000-40865800	Weak transcription	Brain Hippocampus Middle	brain
8	chr21:40856800-40874000	Weak transcription	Aorta	Aorta
9	chr21:40857000-40874200	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr21:40857200-40874000	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr21:40857200-40874600	Weak transcription	Fetal Heart	heart
12	chr21:40860800-40863400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr21:40861600-40863400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr21:40861600-40872000	Weak transcription	Psoas Muscle	Psoas

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