Variant report

Variant	rs61990345
Chromosome Location	chr14:42194649-42194650
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1597049	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1597050	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17112192	0.94[ASN][1000 genomes]
rs17181601	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17181608	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17181615	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17181622	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17181636	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17781361	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41319550	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4584739	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4586337	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4603462	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4624078	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58373729	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs58844543	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs59082466	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59348864	0.80[ASN][1000 genomes]
rs61990312	0.87[AFR][1000 genomes]
rs61990335	0.94[ASN][1000 genomes]
rs61990337	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61990338	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61990339	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61990342	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61990343	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61990346	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61990347	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61990349	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61992404	1.00[ASN][1000 genomes]
rs61992433	0.87[ASN][1000 genomes]
rs72686527	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72686528	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1047300	chr14:41671653-42361098	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv533968	chr14:41882101-42327882	Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	esv2758353	chr14:42045873-42259511	Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	esv2759983	chr14:42045873-42259511	ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv901738	chr14:42145461-42302552	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv901739	chr14:42194373-42270916	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs61990345	LRFN5	cis	thalamus	BrainEAC
rs61990345	LRFN5	cis	intralobular white matter	BrainEAC
rs61990345	LRFN5	cis	frontal cortex	BrainEAC
rs61990345	LRFN5	cis	inferior olivary nucleus	BrainEAC
rs61990345	LRFN5	cis	substantia nigra	BrainEAC
rs61990345	LRFN5	cis	brain	BrainEAC
rs61990345	LRFN5	cis	putamen	BrainEAC
rs61990345	LRFN5	cis	temporal cortex	BrainEAC
rs61990345	LRFN5	cis	hippocampus	BrainEAC
rs61990345	LRFN5	cis	occipital cortex	BrainEAC

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:42188200-42197000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr14:42188400-42198400	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr14:42193400-42197200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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