Variant report

Variant	rs2424585
Chromosome Location	chr20:23626037-23626038
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:23615491..23618366-chr20:23625789..23627708,2	MCF-7	breast:
2	chr20:23615462..23617688-chr20:23624542..23627030,2	MCF-7	breast:
3	chr20:23610829..23612765-chr20:23625069..23626806,2	MCF-7	breast:

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs2145232	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2405368	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2424584	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2424586	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55656752	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55724037	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6114211	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6114215	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73102333	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73102335	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73102352	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73102353	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73102358	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73102363	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73102364	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73102366	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73102376	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73102379	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73102381	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73102386	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs747924	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8116240	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8116249	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8122922	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8122969	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8124308	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491876	chr20:23436633-24031374	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2424585	CST3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:23618800-23626400	Weak transcription	Primary hematopoietic stem cells	blood
2	chr20:23618800-23628600	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr20:23622200-23636600	Weak transcription	Pancreas	Pancrea
4	chr20:23622800-23640000	Weak transcription	Stomach Mucosa	stomach
5	chr20:23623000-23634200	Weak transcription	Right Atrium	heart
6	chr20:23623200-23626800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr20:23623200-23636200	Weak transcription	Lung	lung
8	chr20:23623600-23626800	Weak transcription	NHEK	skin
9	chr20:23623600-23627200	Weak transcription	HMEC	breast
10	chr20:23623800-23626600	Weak transcription	HUVEC	blood vessel
11	chr20:23623800-23627000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr20:23624200-23633000	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr20:23624400-23626600	Weak transcription	Fetal Muscle Leg	muscle
14	chr20:23624400-23627400	Weak transcription	HepG2	liver
15	chr20:23624600-23626800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr20:23624600-23633000	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr20:23625000-23626400	Weak transcription	Fetal Thymus	thymus
18	chr20:23625000-23626600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr20:23625000-23626600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr20:23625000-23627400	Enhancers	GM12878-XiMat	blood
21	chr20:23625000-23627600	Enhancers	Monocytes-CD14+_RO01746	blood
22	chr20:23625600-23626800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr20:23625800-23626800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr20:23626000-23626200	Enhancers	Gastric	stomach
25	chr20:23626000-23627400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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