Variant report

Variant	rs16984411
Chromosome Location	chr20:22748843-22748844
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs16984435	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56896182	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57154892	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58242823	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59207044	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60445726	1.00[AMR][1000 genomes]
rs61540052	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7261797	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7266128	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1061382	chr20:22706041-22763200	ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv544213	chr20:22722740-22791150	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv528221	chr20:22732749-22767280	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16984411	CST3	cis	lymphoblastoid	seeQTL

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:22737800-22749000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr20:22743200-22751400	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr20:22744600-22749000	Weak transcription	NH-A	brain
4	chr20:22744600-22749200	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr20:22745200-22749400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr20:22745400-22750800	Weak transcription	Hela-S3	cervix
7	chr20:22745400-22752400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr20:22745400-22752400	Weak transcription	Gastric	stomach
9	chr20:22745600-22749000	Weak transcription	HSMMtube	muscle
10	chr20:22745800-22749400	Weak transcription	Stomach Mucosa	stomach
11	chr20:22746000-22749000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr20:22746000-22749000	Weak transcription	Ovary	ovary
13	chr20:22746000-22749000	Weak transcription	HMEC	breast
14	chr20:22746000-22749200	Weak transcription	NHEK	skin
15	chr20:22746000-22749400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr20:22746000-22751000	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr20:22746000-22756000	Weak transcription	Spleen	Spleen
18	chr20:22747800-22751400	Enhancers	Placenta	Placenta
19	chr20:22748000-22749600	Enhancers	Placenta Amnion	Placenta Amnion
20	chr20:22748200-22750400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr20:22748600-22750400	Enhancers	HSMM	muscle
22	chr20:22748800-22749000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr20:22748800-22749000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr20:22748800-22749400	Enhancers	A549	lung
25	chr20:22748800-22749600	Enhancers	Fetal Muscle Leg	muscle
26	chr20:22748800-22749800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr20:22748800-22750200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr20:22748800-22750400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr20:22748800-22750400	Enhancers	NHDF-Ad	bronchial
30	chr20:22748800-22751600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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