Variant report

Variant	rs55939301
Chromosome Location	chr5:43272127-43272128
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:43272071..43275298-chr5:43277638..43280213,3	K562	blood:
2	chr5:43268161..43270629-chr5:43271239..43274224,3	K562	blood:
3	chr5:43271201..43273995-chr5:43287069..43290020,2	K562	blood:

Variant related genes	Relation type
ENSG00000261604	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10512825	0.82[ASN][1000 genomes]
rs10805672	0.82[ASN][1000 genomes]
rs10805673	0.81[ASN][1000 genomes]
rs10805674	0.81[ASN][1000 genomes]
rs10941620	0.89[ASN][1000 genomes]
rs10941621	0.82[ASN][1000 genomes]
rs10941622	0.82[ASN][1000 genomes]
rs10941623	0.82[ASN][1000 genomes]
rs10941628	0.82[ASN][1000 genomes]
rs10941630	0.81[ASN][1000 genomes]
rs11738086	0.81[ASN][1000 genomes]
rs11739009	0.82[ASN][1000 genomes]
rs11739665	0.82[ASN][1000 genomes]
rs11740128	0.89[ASN][1000 genomes]
rs11741246	0.82[ASN][1000 genomes]
rs11742712	0.82[ASN][1000 genomes]
rs11743633	0.80[ASN][1000 genomes]
rs11746629	0.89[ASN][1000 genomes]
rs11747834	0.82[ASN][1000 genomes]
rs11951584	0.81[ASN][1000 genomes]
rs12189016	0.82[ASN][1000 genomes]
rs12189447	0.82[ASN][1000 genomes]
rs12514393	0.82[ASN][1000 genomes]
rs12514399	0.82[ASN][1000 genomes]
rs12515072	0.82[ASN][1000 genomes]
rs12518032	0.82[ASN][1000 genomes]
rs12519554	0.89[ASN][1000 genomes]
rs12520012	0.82[ASN][1000 genomes]
rs12522178	0.82[ASN][1000 genomes]
rs13659	0.82[ASN][1000 genomes]
rs1545753	0.82[ASN][1000 genomes]
rs1548097	0.82[ASN][1000 genomes]
rs1564196	0.82[ASN][1000 genomes]
rs1564197	0.82[ASN][1000 genomes]
rs2126948	0.82[ASN][1000 genomes]
rs2126949	0.82[ASN][1000 genomes]
rs2169781	0.82[ASN][1000 genomes]
rs35231094	0.89[ASN][1000 genomes]
rs35239179	0.82[ASN][1000 genomes]
rs3733769	0.82[ASN][1000 genomes]
rs4050485	0.80[ASN][1000 genomes]
rs4320264	0.82[ASN][1000 genomes]
rs4373285	0.82[ASN][1000 genomes]
rs4395639	0.89[ASN][1000 genomes]
rs4443426	0.87[ASN][1000 genomes]
rs4574553	0.82[ASN][1000 genomes]
rs4591755	0.82[ASN][1000 genomes]
rs4866737	0.82[ASN][1000 genomes]
rs4866738	0.82[ASN][1000 genomes]
rs4866813	0.82[ASN][1000 genomes]
rs55634155	0.80[ASN][1000 genomes]
rs55647314	0.83[ASN][1000 genomes]
rs55794239	0.82[ASN][1000 genomes]
rs55800451	0.89[ASN][1000 genomes]
rs55820064	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56023994	0.83[ASN][1000 genomes]
rs56029402	0.89[ASN][1000 genomes]
rs56071328	0.82[ASN][1000 genomes]
rs56114604	0.82[ASN][1000 genomes]
rs56331753	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57392430	0.89[ASN][1000 genomes]
rs57401732	0.82[ASN][1000 genomes]
rs58679159	0.82[ASN][1000 genomes]
rs59078439	0.82[ASN][1000 genomes]
rs60445501	0.82[ASN][1000 genomes]
rs66585077	0.89[ASN][1000 genomes]
rs66691321	0.82[ASN][1000 genomes]
rs67415672	0.88[ASN][1000 genomes]
rs67497876	0.82[ASN][1000 genomes]
rs67651757	0.82[ASN][1000 genomes]
rs67817333	0.82[ASN][1000 genomes]
rs6814	0.82[ASN][1000 genomes]
rs6863246	0.81[ASN][1000 genomes]
rs6887351	0.81[ASN][1000 genomes]
rs7380703	0.84[ASN][1000 genomes]
rs7720165	0.82[ASN][1000 genomes]
rs7734293	0.89[ASN][1000 genomes]
rs922439	0.81[ASN][1000 genomes]
rs9790987	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023741	chr5:42768215-43348145	Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
2	nsv537737	chr5:42768215-43348145	Genic enhancers Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
3	nsv1024636	chr5:42959979-43295782	Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	283 gene(s)	inside rSNPs	diseases
4	nsv537739	chr5:42959979-43295782	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	283 gene(s)	inside rSNPs	diseases
5	nsv508352	chr5:43237830-43391062	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs55939301	NNT	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:43246600-43281400	Weak transcription	Brain Hippocampus Middle	brain
2	chr5:43257400-43274400	Weak transcription	Brain Anterior Caudate	brain
3	chr5:43269000-43273000	Weak transcription	GM12878-XiMat	blood
4	chr5:43270200-43277400	Weak transcription	Brain Angular Gyrus	brain
5	chr5:43271200-43273600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr5:43271200-43280200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr5:43271400-43273800	Weak transcription	NHEK	skin

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