Variant report

Variant	rs8116240
Chromosome Location	chr20:23632730-23632731
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:23619975..23621824-chr20:23630879..23635181,3	MCF-7	breast:

Extended variants
information (count: 28 )
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];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2405368	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2424584	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2424585	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2424586	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55656752	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55724037	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6114211	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6114215	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73102333	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73102335	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73102352	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73102353	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73102358	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73102363	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73102364	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73102366	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73102376	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73102379	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73102381	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73102386	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs747924	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8116249	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8122922	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8122969	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8124308	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	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
2	esv3447058	chr20:23631152-23633850	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs8116240	CST3	Cis_1M	lymphoblastoid	RTeQTL
rs8116240	CST3	cis	multi-tissue	Pritchard

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:23622200-23636600	Weak transcription	Pancreas	Pancrea
2	chr20:23622800-23640000	Weak transcription	Stomach Mucosa	stomach
3	chr20:23623000-23634200	Weak transcription	Right Atrium	heart
4	chr20:23623200-23636200	Weak transcription	Lung	lung
5	chr20:23624200-23633000	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr20:23624600-23633000	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr20:23627600-23633000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr20:23627600-23633000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr20:23627600-23633400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr20:23628200-23633400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr20:23628200-23633600	Weak transcription	Fetal Thymus	thymus
12	chr20:23628200-23638000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr20:23628600-23633000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr20:23631000-23633000	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr20:23631400-23633000	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr20:23631800-23633000	Weak transcription	HepG2	liver
17	chr20:23631800-23633200	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr20:23632400-23633000	Weak transcription	HMEC	breast

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