Variant report

Variant	rs269505
Chromosome Location	chr5:114685541-114685542
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:114679467..114681719-chr5:114684783..114686462,2	MCF-7	breast:
2	chr5:114674153..114676680-chr5:114683585..114685704,2	K562	blood:
3	chr5:114684315..114686804-chr5:114699761..114703151,3	MCF-7	breast:
4	chr5:114684923..114687341-chr5:114688563..114690292,2	MCF-7	breast:

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10447263	0.80[EUR][1000 genomes]
rs10463669	0.86[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs10519405	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10519406	0.93[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11241320	0.93[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs11241323	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs12516512	0.87[CEU][hapmap]
rs12519220	0.88[CEU][hapmap]
rs12654590	0.87[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs12657417	0.92[CEU][hapmap];0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs166566	0.93[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2591258	0.81[EUR][1000 genomes]
rs2605179	0.81[EUR][1000 genomes]
rs269503	0.90[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs269504	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs269506	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs269510	0.96[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs4705524	0.81[EUR][1000 genomes]
rs4705733	0.87[CEU][hapmap];0.86[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs7715232	0.87[CEU][hapmap]

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	nsv916273	chr5:114656592-115089901	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs269505	MCC	cis	cerebellum	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:114679000-114686000	Weak transcription	Pancreas	Pancrea
2	chr5:114683600-114685600	Enhancers	Stomach Mucosa	stomach
3	chr5:114683600-114685800	Enhancers	Duodenum Mucosa	Duodenum
4	chr5:114683800-114685600	Enhancers	Rectal Mucosa Donor 31	rectum
5	chr5:114684000-114686000	Enhancers	Pancreatic Islets	Pancreatic Islet
6	chr5:114684000-114686000	Enhancers	HepG2	liver
7	chr5:114684000-114686200	Enhancers	Fetal Intestine Small	intestine
8	chr5:114684000-114686200	Enhancers	Sigmoid Colon	Sigmoid Colon
9	chr5:114684200-114685800	Enhancers	Liver	Liver
10	chr5:114684400-114685800	Enhancers	HUVEC	blood vessel
11	chr5:114684400-114685800	Enhancers	NH-A	brain
12	chr5:114684400-114686000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr5:114684400-114686000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr5:114684400-114686000	Enhancers	Fetal Intestine Large	intestine
15	chr5:114684400-114686200	Enhancers	Skeletal Muscle Female	skeletal muscle
16	chr5:114684400-114688000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr5:114684600-114685800	Enhancers	Brain Angular Gyrus	brain
18	chr5:114684600-114686000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr5:114684600-114686000	Enhancers	Osteobl	bone
20	chr5:114684600-114686200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr5:114684600-114686200	Enhancers	HSMM	muscle
22	chr5:114684600-114687800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr5:114684600-114688000	Enhancers	Hela-S3	cervix
24	chr5:114684800-114685600	Flanking Active TSS	A549	lung
25	chr5:114684800-114685800	Enhancers	Skeletal Muscle Male	skeletal muscle
26	chr5:114684800-114686000	Enhancers	HMEC	breast
27	chr5:114684800-114686000	Enhancers	NHEK	skin
28	chr5:114684800-114686000	Enhancers	NHLF	lung
29	chr5:114684800-114686200	Enhancers	HSMMtube	muscle
30	chr5:114684800-114687400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr5:114685000-114685800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr5:114685000-114686000	Enhancers	Brain Substantia Nigra	brain
33	chr5:114685200-114685600	Enhancers	K562	blood
34	chr5:114685200-114685800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr5:114685200-114686000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr5:114685400-114685600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr5:114685400-114685600	Enhancers	Brain Anterior Caudate	brain
38	chr5:114685400-114685800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
39	chr5:114685400-114685800	Flanking Active TSS	NHDF-Ad	bronchial
40	chr5:114685400-114686000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr5:114685400-114686400	Enhancers	Ovary	ovary
42	chr5:114685400-114686600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr5:114685400-114691400	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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