Variant report

Variant	rs10058862
Chromosome Location	chr5:54122581-54122582
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:54122100..54123880-chr5:54124518..54126459,2	MCF-7	breast:

Extended variants
information (count: 133 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:131)

rs_ID	r²[population]
rs10036257	1.00[ASN][1000 genomes]
rs10036606	1.00[ASN][1000 genomes]
rs10039924	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10042288	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10042394	1.00[ASN][1000 genomes]
rs10042495	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10043408	0.90[ASN][1000 genomes]
rs10045175	1.00[ASN][1000 genomes]
rs10045765	1.00[ASN][1000 genomes]
rs10045790	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10050561	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10053168	0.97[ASN][1000 genomes]
rs10056452	0.80[EUR][1000 genomes]
rs10057871	1.00[ASN][1000 genomes]
rs10058571	1.00[ASN][1000 genomes]
rs10061958	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10066294	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10066622	1.00[ASN][1000 genomes]
rs10066683	0.81[ASN][1000 genomes]
rs10068073	0.88[ASN][1000 genomes]
rs10071183	0.89[ASN][1000 genomes]
rs10073662	0.89[ASN][1000 genomes]
rs10073721	0.89[ASN][1000 genomes]
rs10434559	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10461588	0.97[ASN][1000 genomes]
rs10471923	1.00[ASN][1000 genomes]
rs1073709	1.00[ASN][1000 genomes]
rs10737956	0.92[ASN][1000 genomes]
rs10805463	0.97[ASN][1000 genomes]
rs10805468	0.89[ASN][1000 genomes]
rs10805469	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10940427	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10940428	1.00[ASN][1000 genomes]
rs10940431	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs10940432	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs10940434	0.80[EUR][1000 genomes]
rs11738151	0.80[EUR][1000 genomes]
rs11742711	0.83[EUR][1000 genomes]
rs11950757	0.86[ASN][1000 genomes]
rs11952681	0.96[ASN][1000 genomes]
rs11959080	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12514244	1.00[ASN][1000 genomes]
rs12515327	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12520494	0.98[ASN][1000 genomes]
rs12522199	1.00[ASN][1000 genomes]
rs12657845	0.83[EUR][1000 genomes]
rs13155441	1.00[ASN][1000 genomes]
rs13161386	0.96[ASN][1000 genomes]
rs13161718	0.96[ASN][1000 genomes]
rs13167527	1.00[ASN][1000 genomes]
rs13171964	0.96[ASN][1000 genomes]
rs13173669	1.00[ASN][1000 genomes]
rs13180287	1.00[ASN][1000 genomes]
rs13186826	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1560165	0.84[CEU][hapmap];0.80[EUR][1000 genomes]
rs1560166	0.84[CEU][hapmap];0.80[EUR][1000 genomes]
rs2017082	0.84[CEU][hapmap];0.84[GIH][hapmap]
rs2019005	0.84[CEU][hapmap];0.80[EUR][1000 genomes]
rs2195392	0.84[CEU][hapmap]
rs2195393	0.84[CEU][hapmap]
rs3916738	0.83[EUR][1000 genomes]
rs3935813	0.91[EUR][1000 genomes]
rs4074332	0.86[JPT][hapmap]
rs4242044	0.89[ASN][1000 genomes]
rs4242045	1.00[ASN][1000 genomes]
rs4242046	0.98[ASN][1000 genomes]
rs4242047	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4242048	0.96[ASN][1000 genomes]
rs4282277	0.88[ASN][1000 genomes]
rs4289528	0.98[ASN][1000 genomes]
rs4290968	0.97[ASN][1000 genomes]
rs4292417	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4298212	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4320207	0.98[ASN][1000 genomes]
rs4336310	0.97[ASN][1000 genomes]
rs4336311	0.96[ASN][1000 genomes]
rs4356994	0.89[ASN][1000 genomes]
rs4362906	1.00[ASN][1000 genomes]
rs4437335	0.96[ASN][1000 genomes]
rs4446420	0.88[EUR][1000 genomes]
rs4451013	0.97[ASN][1000 genomes]
rs4451014	0.96[ASN][1000 genomes]
rs4457032	0.97[ASN][1000 genomes]
rs4498213	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4505913	0.88[ASN][1000 genomes]
rs4515247	0.80[EUR][1000 genomes]
rs4519880	1.00[ASN][1000 genomes]
rs4527555	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4527556	1.00[ASN][1000 genomes]
rs4582235	0.96[ASN][1000 genomes]
rs4591702	1.00[ASN][1000 genomes]
rs4610422	1.00[ASN][1000 genomes]
rs4645296	0.93[ASN][1000 genomes]
rs4865586	0.86[JPT][hapmap]
rs4865870	0.88[ASN][1000 genomes]
rs4865872	0.89[ASN][1000 genomes]
rs4865873	0.97[ASN][1000 genomes]
rs4865874	0.97[ASN][1000 genomes]
rs4865875	1.00[ASN][1000 genomes]
rs4865876	1.00[ASN][1000 genomes]
rs4865877	0.96[ASN][1000 genomes]
rs4865880	0.82[EUR][1000 genomes]
rs4865882	0.80[EUR][1000 genomes]
rs59664922	0.82[ASN][1000 genomes]
rs6450248	0.82[ASN][1000 genomes]
rs6450251	1.00[ASN][1000 genomes]
rs6450252	1.00[ASN][1000 genomes]
rs6450253	1.00[ASN][1000 genomes]
rs6860729	0.88[ASN][1000 genomes]
rs6860824	0.86[JPT][hapmap]
rs6863705	1.00[CEU][hapmap];0.88[CHB][hapmap];0.90[CHD][hapmap];0.92[JPT][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes]
rs6867867	0.89[ASN][1000 genomes]
rs6887578	0.96[ASN][1000 genomes]
rs6892315	0.89[ASN][1000 genomes]
rs6899052	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73126822	0.82[ASN][1000 genomes]
rs73126828	0.82[ASN][1000 genomes]
rs73126830	0.82[ASN][1000 genomes]
rs7446423	1.00[ASN][1000 genomes]
rs7446869	0.96[ASN][1000 genomes]
rs7709225	0.81[EUR][1000 genomes]
rs7709401	0.81[EUR][1000 genomes]
rs7726707	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7728303	1.00[ASN][1000 genomes]
rs7728418	0.82[ASN][1000 genomes]
rs7731103	0.97[ASN][1000 genomes]
rs9292072	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9292073	0.89[ASN][1000 genomes]
rs9292074	1.00[ASN][1000 genomes]
rs9687636	1.00[ASN][1000 genomes]
rs9968754	0.98[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	nsv830300	chr5:54056300-54257344	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	esv3358092	chr5:54077828-54189150	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10058862	ARL15	cis	cerebellum	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:54117200-54138000	Weak transcription	Aorta	Aorta
2	chr5:54117600-54126800	Weak transcription	NHLF	lung
3	chr5:54118000-54126200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr5:54118000-54128600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr5:54118600-54123200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr5:54118600-54129200	Weak transcription	Placenta	Placenta
7	chr5:54120800-54123000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr5:54121200-54123000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr5:54121600-54127400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr5:54121800-54122800	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr5:54122400-54125400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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