Variant report

Variant	rs6859962
Chromosome Location	chr5:126438601-126438602
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 74 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10035217	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10037625	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10038644	0.86[EUR][1000 genomes]
rs10041457	0.86[EUR][1000 genomes]
rs10051184	0.82[EUR][1000 genomes]
rs10062622	0.83[EUR][1000 genomes]
rs108558	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11241913	0.85[CEU][hapmap]
rs11241916	0.86[EUR][1000 genomes]
rs12654947	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12655220	0.85[CEU][hapmap]
rs12659065	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13178353	0.90[EUR][1000 genomes]
rs13190493	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1543815	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1860440	0.85[EUR][1000 genomes]
rs1860441	0.82[EUR][1000 genomes]
rs2041318	0.82[CEU][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2109215	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2191209	0.82[JPT][hapmap]
rs2408788	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2408789	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2408790	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs248040	0.96[CEU][hapmap];0.91[JPT][hapmap]
rs248042	0.82[EUR][1000 genomes]
rs248062	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs248081	0.91[JPT][hapmap]
rs248091	0.80[EUR][1000 genomes]
rs248092	0.86[EUR][1000 genomes]
rs248095	0.85[EUR][1000 genomes]
rs248096	0.85[EUR][1000 genomes]
rs248101	0.83[EUR][1000 genomes]
rs248102	0.85[EUR][1000 genomes]
rs248105	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs248107	0.83[CEU][hapmap];0.80[CHB][hapmap];0.96[JPT][hapmap];0.85[EUR][1000 genomes]
rs248108	0.85[EUR][1000 genomes]
rs248109	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs248113	0.96[CEU][hapmap];0.83[JPT][hapmap];0.91[EUR][1000 genomes]
rs248118	0.91[EUR][1000 genomes]
rs248121	0.91[EUR][1000 genomes]
rs248126	0.89[EUR][1000 genomes]
rs2585204	0.89[EUR][1000 genomes]
rs3915634	0.86[EUR][1000 genomes]
rs3936304	0.83[EUR][1000 genomes]
rs3936305	0.83[EUR][1000 genomes]
rs4380710	0.85[CEU][hapmap]
rs4455612	0.83[EUR][1000 genomes]
rs4836310	0.85[EUR][1000 genomes]
rs4836313	0.85[EUR][1000 genomes]
rs57555006	0.88[EUR][1000 genomes]
rs6595746	0.82[EUR][1000 genomes]
rs6861348	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6864668	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6873502	0.86[EUR][1000 genomes]
rs6875043	0.83[EUR][1000 genomes]
rs6879393	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6881948	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6883106	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6883627	0.86[EUR][1000 genomes]
rs6883672	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6884988	0.85[EUR][1000 genomes]
rs6898415	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs726990	0.89[EUR][1000 genomes]
rs727038	0.82[CEU][hapmap];0.82[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs758628	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7731621	0.82[JPT][hapmap]
rs7734890	0.85[EUR][1000 genomes]
rs9687751	0.82[EUR][1000 genomes]
rs9687752	0.82[EUR][1000 genomes]
rs990743	0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024265	chr5:126213004-126691163	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv869897	chr5:126224358-126445210	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1033607	chr5:126385181-127304459	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	esv1816248	chr5:126399039-126486539	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6859962	C5orf63	cis	Artery Tibial	GTEx
rs6859962	MARCH3	cis	Muscle Skeletal	GTEx
rs6859962	C5orf63	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:126433400-126444200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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