Variant report

Variant	rs12561820
Chromosome Location	chr1:173573652-173573653
allele	C/T
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	SPI1	chr1:173573374-173573827	HL-60	blood:	n/a	chr1:173573600-173573613 chr1:173573730-173573743

Variant related genes	Relation type
SLC9C2	TF binding region

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10798290	0.85[ASN][1000 genomes]
rs10798291	0.87[ASN][1000 genomes]
rs10798292	0.87[ASN][1000 genomes]
rs10912651	0.81[ASN][1000 genomes]
rs12032386	0.85[ASN][1000 genomes]
rs12032790	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12039524	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12041743	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12042027	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12065988	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12092383	0.95[CEU][hapmap]
rs12568477	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2422467	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2901747	0.87[ASN][1000 genomes]
rs2901748	0.87[ASN][1000 genomes]
rs34754266	0.85[ASN][1000 genomes]
rs56138893	0.83[EUR][1000 genomes]
rs58287165	0.85[EUR][1000 genomes]
rs59858609	0.86[EUR][1000 genomes]
rs61826760	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61826764	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61826765	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61826766	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61826768	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61826769	0.85[AFR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61826805	0.85[EUR][1000 genomes]
rs61826806	0.86[EUR][1000 genomes]
rs61826809	0.82[EUR][1000 genomes]
rs61828911	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs61828913	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs61828914	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs61828922	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61828923	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6425251	0.87[ASN][1000 genomes]
rs6674589	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6681766	0.82[EUR][1000 genomes]
rs72709357	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs727924	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7513933	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7552723	0.87[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12561820	CLN5	trans	lymphoblastoid	RTeQTL

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:173572200-173574000	Enhancers	Primary hematopoietic stem cells short term culture	blood
2	chr1:173572800-173574000	Enhancers	K562	blood
3	chr1:173572800-173574600	Weak transcription	Psoas Muscle	Psoas
4	chr1:173573000-173577600	Weak transcription	Right Atrium	heart
5	chr1:173573400-173586000	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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