Variant report

Variant	rs2166355
Chromosome Location	chr5:54051901-54051902
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:54037732..54040168-chr5:54049770..54052180,2	MCF-7	breast:
2	chr5:54044170..54046541-chr5:54049727..54052446,2	MCF-7	breast:
3	chr5:54049724..54052539-chr5:54057510..54059343,2	K562	blood:

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs13436904	0.80[EUR][1000 genomes]
rs13436919	0.80[EUR][1000 genomes]
rs17346285	0.93[EUR][1000 genomes]
rs2121130	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35463987	0.93[EUR][1000 genomes]
rs4274943	0.80[EUR][1000 genomes]
rs4355479	0.80[EUR][1000 genomes]
rs4380600	0.80[EUR][1000 genomes]
rs4425466	0.95[CEU][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.92[TSI][hapmap];0.94[EUR][1000 genomes]
rs4472223	0.83[EUR][1000 genomes]
rs4526067	0.82[EUR][1000 genomes]
rs4572962	0.90[CEU][hapmap];0.93[EUR][1000 genomes]
rs55728436	0.84[EUR][1000 genomes]
rs55944106	0.82[EUR][1000 genomes]
rs56145198	0.83[EUR][1000 genomes]
rs56202300	0.94[EUR][1000 genomes]
rs56207018	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56298453	0.82[EUR][1000 genomes]
rs56386053	0.94[EUR][1000 genomes]
rs57059470	0.82[EUR][1000 genomes]
rs60775366	0.80[EUR][1000 genomes]
rs6450249	0.83[EUR][1000 genomes]
rs66533726	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs66599423	0.92[EUR][1000 genomes]
rs66812968	0.84[EUR][1000 genomes]
rs67510332	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6867643	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6876730	0.80[EUR][1000 genomes]
rs6897534	0.86[EUR][1000 genomes]
rs72757444	0.83[EUR][1000 genomes]
rs72757446	0.83[EUR][1000 genomes]
rs72760107	0.80[EUR][1000 genomes]
rs7710436	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7734384	0.80[EUR][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	nsv880717	chr5:54025701-54106378	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2166355	ARL15	cis	cerebellum	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:54040600-54052400	Weak transcription	Brain Hippocampus Middle	brain
2	chr5:54041800-54052000	Weak transcription	Placenta	Placenta
3	chr5:54041800-54052200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr5:54042600-54053800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr5:54044800-54056000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr5:54048600-54054600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr5:54049000-54053600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr5:54049000-54056200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr5:54049200-54052000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr5:54049200-54052200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr5:54049200-54052600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr5:54049200-54056200	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr5:54049200-54057000	Weak transcription	Fetal Heart	heart
14	chr5:54049400-54052000	Weak transcription	Primary monocytes fromperipheralblood	blood
15	chr5:54049400-54052000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr5:54049400-54052600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr5:54049400-54052800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr5:54049400-54052800	Weak transcription	HSMMtube	muscle
19	chr5:54049400-54052800	Weak transcription	Osteobl	bone
20	chr5:54049400-54053200	Enhancers	Primary B cells from peripheral blood	blood
21	chr5:54049400-54053400	Weak transcription	HSMM	muscle
22	chr5:54049400-54055200	Weak transcription	Aorta	Aorta
23	chr5:54049400-54056400	Weak transcription	Left Ventricle	heart
24	chr5:54049600-54052000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr5:54049600-54052200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr5:54049600-54052600	Weak transcription	NHDF-Ad	bronchial
27	chr5:54050000-54052800	Weak transcription	NHLF	lung
28	chr5:54050600-54053000	Enhancers	Primary B cells from cord blood	blood
29	chr5:54050800-54053000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
30	chr5:54051000-54052200	Weak transcription	Lung	lung
31	chr5:54051000-54052800	Weak transcription	NH-A	brain
32	chr5:54051000-54053600	Enhancers	Primary T helper cells PMA-I stimulated	--
33	chr5:54051600-54052800	Enhancers	Esophagus	oesophagus
34	chr5:54051600-54053000	Enhancers	Primary T helper naive cells from peripheral blood	blood
35	chr5:54051600-54053000	Enhancers	Primary T helper cells fromperipheralblood	blood
36	chr5:54051800-54052000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr5:54051800-54052000	Enhancers	Primary T killer memory cells from peripheral blood	blood
38	chr5:54051800-54052000	Enhancers	K562	blood
39	chr5:54051800-54052000	Enhancers	Monocytes-CD14+_RO01746	blood
40	chr5:54051800-54052800	Enhancers	GM12878-XiMat	blood
41	chr5:54051800-54053000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
42	chr5:54051800-54053000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
43	chr5:54051800-54053200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
44	chr5:54051800-54053200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
45	chr5:54051800-54053400	Enhancers	Primary T cells fromperipheralblood	blood
46	chr5:54051800-54053800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr5:54051800-54053800	Enhancers	HMEC	breast

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