Variant report

Variant	rs61826766
Chromosome Location	chr1:173631181-173631182
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TRIM28	chr1:173631001-173631259	K562	blood:	n/a	n/a
2	ZNF384	chr1:173631010-173631208	K562	blood:	n/a	n/a
3	CBX3	chr1:173630918-173631302	K562	blood:	n/a	n/a
4	ZNF143	chr1:173630971-173631201	K562	blood:	n/a	n/a
5	POLR2A	chr1:173631021-173631242	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:173625902..173627513-chr1:173630410..173632425,2	K562	blood:

Variant related genes	Relation type
ENSG00000238430	TF binding region

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10798290	0.81[ASN][1000 genomes]
rs12032386	0.81[ASN][1000 genomes]
rs12032790	0.80[ASN][1000 genomes]
rs12039524	0.83[ASN][1000 genomes]
rs12041743	0.80[ASN][1000 genomes]
rs12042027	0.80[ASN][1000 genomes]
rs12065988	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12561820	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12568477	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2422467	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34754266	0.81[ASN][1000 genomes]
rs56138893	0.90[EUR][1000 genomes]
rs58287165	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs59858609	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61826760	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61826764	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61826765	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61826768	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61826769	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61826805	0.92[EUR][1000 genomes]
rs61826806	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61826809	0.88[EUR][1000 genomes]
rs61826810	0.85[EUR][1000 genomes]
rs61828913	0.80[ASN][1000 genomes]
rs61828914	0.81[ASN][1000 genomes]
rs61828922	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61828923	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6674589	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6681766	0.88[EUR][1000 genomes]
rs72709357	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs727924	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7513933	0.96[EUR][1000 genomes];0.98[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
rs61826766	CLN5	trans	lymphoblastoid	RTeQTL

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:173623600-173637400	Weak transcription	Brain Anterior Caudate	brain
2	chr1:173625400-173638400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr1:173626000-173637600	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr1:173626200-173637400	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr1:173626200-173637400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr1:173626400-173637200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr1:173626400-173637400	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr1:173630600-173646600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr1:173630800-173636000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr1:173631000-173632000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr1:173631000-173636000	Weak transcription	NHEK	skin
12	chr1:173631000-173638600	Weak transcription	HMEC	breast

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