Variant report

Variant	rs2145231
Chromosome Location	chr20:23625547-23625548
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:23615462..23617688-chr20:23624542..23627030,2	MCF-7	breast:
2	chr20:23610829..23612765-chr20:23625069..23626806,2	MCF-7	breast:
3	chr20:23624045..23625707-chr20:23633322..23636030,2	MCF-7	breast:

Extended variants
information (count: 9 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs13037020	1.00[CEU][hapmap];0.96[TSI][hapmap];0.96[EUR][1000 genomes]
rs13039144	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2104005	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2254635	0.83[TSI][hapmap]
rs2405367	0.83[TSI][hapmap]
rs6036481	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6114213	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6114214	0.93[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2145231	CST3	cis	cerebellum	SCAN
rs2145231	NANP	cis	cerebellum	SCAN
rs2145231	CST3	cis	parietal	SCAN
rs2145231	CST3	cis	lymphoblastoid	seeQTL
rs2145231	CST3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:23618600-23626000	Weak transcription	Gastric	stomach
2	chr20:23618800-23626400	Weak transcription	Primary hematopoietic stem cells	blood
3	chr20:23618800-23628600	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr20:23622000-23625600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr20:23622200-23636600	Weak transcription	Pancreas	Pancrea
6	chr20:23622800-23640000	Weak transcription	Stomach Mucosa	stomach
7	chr20:23623000-23634200	Weak transcription	Right Atrium	heart
8	chr20:23623200-23626800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr20:23623200-23636200	Weak transcription	Lung	lung
10	chr20:23623400-23625600	Enhancers	Skeletal Muscle Female	skeletal muscle
11	chr20:23623600-23626800	Weak transcription	NHEK	skin
12	chr20:23623600-23627200	Weak transcription	HMEC	breast
13	chr20:23623800-23626600	Weak transcription	HUVEC	blood vessel
14	chr20:23623800-23627000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr20:23624200-23633000	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr20:23624400-23626600	Weak transcription	Fetal Muscle Leg	muscle
17	chr20:23624400-23627400	Weak transcription	HepG2	liver
18	chr20:23624600-23626800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr20:23624600-23633000	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr20:23624800-23625600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr20:23625000-23626000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr20:23625000-23626400	Weak transcription	Fetal Thymus	thymus
23	chr20:23625000-23626600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr20:23625000-23626600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr20:23625000-23627400	Enhancers	GM12878-XiMat	blood
26	chr20:23625000-23627600	Enhancers	Monocytes-CD14+_RO01746	blood
27	chr20:23625200-23625600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr20:23625200-23625600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr20:23625400-23625600	Enhancers	H9 Cell Line	embryonic stem cell
30	chr20:23625400-23626000	Enhancers	H1 Cell Line	embryonic stem cell

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