Variant report

Variant	rs1883923
Chromosome Location	chr20:24609565-24609566
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CST7-3	chr20:24608941-24609627	NONHSAT079113

Extended variants
information (count: 32 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12480522	0.85[CEU][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12481129	0.93[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12481146	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17250068	0.85[CEU][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17823746	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1887057	0.93[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2024608	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2026566	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2179800	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2892216	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4813523	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4813524	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4815282	0.93[CEU][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4815286	0.93[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4815287	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4815288	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4815289	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4815290	0.93[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4815291	0.93[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55770994	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58949684	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6036849	0.93[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6036851	0.93[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6036854	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs60869925	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7268862	0.93[CEU][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73345329	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73345369	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73345393	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8118304	1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv9793	chr20:23939613-24734850	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	esv3332519	chr20:24535099-24815615	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:24584400-24612600	Weak transcription	Aorta	Aorta
2	chr20:24600000-24609600	Weak transcription	Brain Angular Gyrus	brain
3	chr20:24602400-24610000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr20:24607800-24611600	Enhancers	Brain Substantia Nigra	brain
5	chr20:24608200-24610000	Enhancers	Primary hematopoietic stem cells short term culture	blood
6	chr20:24608400-24610600	Enhancers	Spleen	Spleen
7	chr20:24608400-24611000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr20:24608400-24611000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
9	chr20:24608400-24611400	Enhancers	Fetal Heart	heart
10	chr20:24608400-24613200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr20:24608600-24611400	Enhancers	Fetal Thymus	thymus
12	chr20:24608600-24615000	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr20:24608800-24609800	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr20:24608800-24610400	Enhancers	Fetal Muscle Trunk	muscle
15	chr20:24608800-24610600	Enhancers	Primary T cells from cord blood	blood
16	chr20:24608800-24611000	Enhancers	Primary hematopoietic stem cells	blood
17	chr20:24608800-24611000	Enhancers	Brain Inferior Temporal Lobe	brain
18	chr20:24608800-24616800	Enhancers	Brain Hippocampus Middle	brain
19	chr20:24609200-24609800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr20:24609200-24610400	Enhancers	Brain Anterior Caudate	brain
21	chr20:24609200-24610600	Enhancers	Fetal Stomach	stomach
22	chr20:24609200-24610600	Enhancers	Left Ventricle	heart
23	chr20:24609200-24615200	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr20:24609400-24609800	Enhancers	Duodenum Mucosa	Duodenum
25	chr20:24609400-24609800	Genic enhancers	Thymus	Thymus
26	chr20:24609400-24610400	Enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr20:24609400-24610400	Enhancers	Right Atrium	heart

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