Variant report

Variant	rs4813524
Chromosome Location	chr20:24612808-24612809
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:24612466..24614630-chr20:24629800..24632618,2	MCF-7	breast:
2	chr20:24610820..24613195-chr8:23266116..23269029,2	MCF-7	breast:
3	chr20:24611712..24613428-chr20:24614096..24616788,2	K562	blood:

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs12480522	0.90[CEU][hapmap];0.90[GIH][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12481129	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12481146	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17250061	0.83[MEX][hapmap]
rs17250068	0.90[CEU][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17823746	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1883923	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1887057	0.95[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2024608	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2026566	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2179800	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2892216	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4813523	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4815282	0.95[CEU][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4815286	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];0.96[MEX][hapmap];0.92[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4815287	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4815288	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4815289	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4815290	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4815291	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55770994	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58949684	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6036849	0.95[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6036851	0.95[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6036854	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6049811	0.80[MEX][hapmap]
rs60869925	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7268862	0.95[CEU][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73345329	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73345369	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73345393	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8118304	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][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	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
3	nsv912824	chr20:24612808-24639916	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4813524	CST5	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:24608400-24613200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr20:24608600-24615000	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr20:24608800-24616800	Enhancers	Brain Hippocampus Middle	brain
4	chr20:24609200-24615200	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr20:24610400-24613400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr20:24610400-24613800	Weak transcription	Brain Anterior Caudate	brain
7	chr20:24610400-24615600	Weak transcription	Right Atrium	heart
8	chr20:24610600-24613200	Weak transcription	Fetal Muscle Leg	muscle
9	chr20:24610600-24613800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr20:24610600-24613800	Weak transcription	Gastric	stomach
11	chr20:24610600-24613800	Weak transcription	Left Ventricle	heart
12	chr20:24610600-24613800	Weak transcription	Lung	lung
13	chr20:24610600-24615000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr20:24610600-24615600	Weak transcription	Right Ventricle	heart
15	chr20:24610800-24615600	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr20:24610800-24615600	Weak transcription	Thymus	Thymus
17	chr20:24611000-24613800	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr20:24611000-24615200	Weak transcription	Primary hematopoietic stem cells	blood
19	chr20:24611000-24615400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr20:24611400-24614400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr20:24611400-24614400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr20:24611400-24615400	Weak transcription	Fetal Thymus	thymus
23	chr20:24611600-24613400	Weak transcription	Brain Substantia Nigra	brain
24	chr20:24612200-24613200	Weak transcription	Brain Cingulate Gyrus	brain
25	chr20:24612600-24614600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr20:24612800-24613600	Weak transcription	Aorta	Aorta
27	chr20:24612800-24614800	Weak transcription	Brain Angular Gyrus	brain

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