Variant report

Variant	rs12065988
Chromosome Location	chr1:173606179-173606180
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:173605287..173609267-chr1:173609597..173614362,5	K562	blood:
2	chr1:173605538..173609079-chr1:173609597..173613461,5	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KLHL20-1	chr1:173605966-173606273	ENSG00000232113.1
2	lnc-KLHL20-1	chr1:173605966-173606330	NONHSAT007643

Extended variants
information (count: 78 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10798290	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs10798291	0.81[ASN][1000 genomes]
rs10798292	0.81[ASN][1000 genomes]
rs10912624	0.81[CHB][hapmap]
rs10912626	0.81[CHB][hapmap]
rs10912643	0.81[CHB][hapmap]
rs10912651	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs10912660	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs10912670	0.81[CHB][hapmap];0.85[YRI][hapmap]
rs10912671	0.90[CHB][hapmap];0.83[YRI][hapmap]
rs12026427	0.81[CHB][hapmap]
rs12026677	0.81[CHB][hapmap]
rs12032790	0.85[ASN][1000 genomes]
rs12037210	0.80[CHB][hapmap]
rs12039524	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12041743	0.85[ASN][1000 genomes]
rs12042027	0.85[ASN][1000 genomes]
rs12065426	0.80[CHB][hapmap]
rs12067170	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs12075071	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs12082131	0.90[CHB][hapmap]
rs12561820	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12561931	0.90[CHB][hapmap]
rs12568477	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12744504	0.81[CHB][hapmap]
rs1461014	0.81[CHB][hapmap]
rs1886639	0.80[CHB][hapmap]
rs2144708	0.90[CHB][hapmap];0.83[YRI][hapmap]
rs2273366	0.90[CHB][hapmap]
rs2422467	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28825469	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2901747	0.81[ASN][1000 genomes]
rs2901748	0.81[ASN][1000 genomes]
rs4539167	0.81[CHB][hapmap]
rs56138893	0.91[EUR][1000 genomes]
rs57592568	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs58287165	0.87[EUR][1000 genomes]
rs59858609	0.88[EUR][1000 genomes]
rs61826760	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61826764	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61826765	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61826766	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61826768	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61826769	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61826805	0.89[EUR][1000 genomes]
rs61826806	0.88[EUR][1000 genomes]
rs61826809	0.89[EUR][1000 genomes]
rs61826810	0.86[EUR][1000 genomes]
rs61828911	0.84[ASN][1000 genomes]
rs61828913	0.85[ASN][1000 genomes]
rs61828914	0.86[ASN][1000 genomes]
rs61828922	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61828923	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6413827	0.90[CHB][hapmap]
rs6425251	1.00[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs6425258	0.90[CHB][hapmap]
rs6660804	0.80[CHB][hapmap]
rs6674589	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6681766	0.94[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes]
rs6687872	0.81[CHB][hapmap]
rs6696680	0.90[CHB][hapmap];0.85[YRI][hapmap]
rs72709357	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs727924	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7513933	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7514556	0.90[CHB][hapmap]
rs7515721	0.90[CHB][hapmap];0.85[YRI][hapmap]
rs7524592	0.81[CHB][hapmap]
rs7525100	0.81[CHB][hapmap]
rs7530469	0.80[CHB][hapmap]
rs7541082	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs7542910	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs7549074	0.81[CHB][hapmap]
rs7552723	0.81[ASN][1000 genomes]
rs7552741	0.90[CHB][hapmap]
rs912767	0.80[CHB][hapmap]
rs9425745	0.90[CHB][hapmap]
rs969029	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs9803671	0.82[AMR][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12065988	CLN5	trans	lymphoblastoid	RTeQTL
rs12065988	SERPINC1	cis	Muscle Skeletal	GTEx

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:173598000-173607000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:173603000-173606200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:173604800-173606800	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr1:173606000-173606200	Enhancers	ES-WA7 Cell Line	embryonic stem cell

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