Variant report

Variant	rs2405368
Chromosome Location	chr20:23627354-23627355
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:23615491..23618366-chr20:23625789..23627708,2	MCF-7	breast:
2	chr20:23616713..23621069-chr20:23626234..23629659,5	K562	blood:

Variant related genes	Relation type
ENSG00000101439	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs2145232	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2424584	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2424585	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2424586	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55656752	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55724037	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6114211	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6114215	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73102333	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73102335	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73102352	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73102353	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73102358	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73102363	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73102364	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73102366	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73102376	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73102379	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73102381	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73102386	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs747924	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8116240	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8116249	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8122922	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8122969	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8124308	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2405368	CST3	Cis_1M	lymphoblastoid	RTeQTL
rs2405368	CST3	cis	multi-tissue	Pritchard

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:23618800-23628600	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr20:23622200-23636600	Weak transcription	Pancreas	Pancrea
3	chr20:23622800-23640000	Weak transcription	Stomach Mucosa	stomach
4	chr20:23623000-23634200	Weak transcription	Right Atrium	heart
5	chr20:23623200-23636200	Weak transcription	Lung	lung
6	chr20:23624200-23633000	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr20:23624400-23627400	Weak transcription	HepG2	liver
8	chr20:23624600-23633000	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr20:23625000-23627400	Enhancers	GM12878-XiMat	blood
10	chr20:23625000-23627600	Enhancers	Monocytes-CD14+_RO01746	blood
11	chr20:23626000-23627400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr20:23626400-23627600	Enhancers	Primary hematopoietic stem cells	blood
13	chr20:23626400-23627600	Enhancers	Fetal Thymus	thymus
14	chr20:23626400-23627800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr20:23626600-23627400	Enhancers	HUVEC	blood vessel
16	chr20:23626600-23627600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr20:23626600-23628600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr20:23626800-23627400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr20:23626800-23627600	Enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr20:23626800-23627600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr20:23626800-23627600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr20:23627000-23627600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr20:23627200-23627600	Enhancers	HMEC	breast

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