Variant report

Variant	rs2422467
Chromosome Location	chr1:173625181-173625182
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10798291	0.81[ASN][1000 genomes]
rs10798292	0.81[ASN][1000 genomes]
rs12032790	0.84[ASN][1000 genomes]
rs12039524	0.87[ASN][1000 genomes]
rs12041743	0.84[ASN][1000 genomes]
rs12042027	0.84[ASN][1000 genomes]
rs12065988	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12561820	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12568477	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2901747	0.81[ASN][1000 genomes]
rs2901748	0.81[ASN][1000 genomes]
rs56138893	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58287165	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59858609	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61826760	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61826764	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61826765	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61826766	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61826768	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61826769	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61826805	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61826806	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61826809	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61826810	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61828911	0.82[ASN][1000 genomes]
rs61828913	0.84[ASN][1000 genomes]
rs61828914	0.85[ASN][1000 genomes]
rs61828922	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61828923	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6425251	0.81[ASN][1000 genomes]
rs6674589	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6681766	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72709357	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs727924	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7513933	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7552723	0.81[ASN][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	nsv1012384	chr1:173614816-173974426	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	294 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2422467	CLN5	trans	lymphoblastoid	RTeQTL

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:173613600-173629800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:173623600-173637400	Weak transcription	Brain Anterior Caudate	brain
3	chr1:173624400-173625600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr1:173624600-173626400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr1:173624800-173625800	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
6	chr1:173624800-173626000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
7	chr1:173624800-173626000	Strong transcription	Cortex derived primary cultured neurospheres	brain
8	chr1:173624800-173626200	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
9	chr1:173624800-173626400	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
10	chr1:173625000-173625200	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
11	chr1:173625000-173625400	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
12	chr1:173625000-173625400	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr1:173625000-173625400	ZNF genes & repeats	Fetal Brain Female	brain
14	chr1:173625000-173625400	ZNF genes & repeats	Ovary	ovary
15	chr1:173625000-173625600	ZNF genes & repeats	Brain Dorsolateral Prefrontal Cortex	brain
16	chr1:173625000-173625800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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