Variant report

Variant	rs2422433
Chromosome Location	chr1:173525079-173525080
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 84 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs1024266	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10399838	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10494490	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10737301	1.00[CHB][hapmap]
rs10737303	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10753078	1.00[CHB][hapmap]
rs10798283	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10798284	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10798285	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10798290	0.87[CEU][hapmap];0.80[CHB][hapmap]
rs10912624	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10912625	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10912626	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10912632	0.89[AMR][1000 genomes]
rs10912634	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10912635	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10912636	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10912641	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10912642	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10912643	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10912651	0.86[CEU][hapmap]
rs11582670	0.82[AMR][1000 genomes]
rs12026427	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12026637	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12026677	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12026993	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12027451	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12027495	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12033623	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12034341	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12034533	0.89[AMR][1000 genomes]
rs12035105	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12037210	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12041114	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12065426	1.00[CHB][hapmap];0.84[CHD][hapmap];0.91[JPT][hapmap]
rs12406352	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12406500	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12744504	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs1461014	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1461023	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1547155	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1547156	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16846113	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16846206	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1886639	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1925340	0.89[AMR][1000 genomes]
rs2017323	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3934575	1.00[CHB][hapmap]
rs3934576	1.00[CHB][hapmap]
rs4244195	1.00[CHB][hapmap]
rs4294450	1.00[CHB][hapmap]
rs4310474	1.00[CHB][hapmap]
rs4336887	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4539167	1.00[CHB][hapmap]
rs4916365	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4916368	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60043192	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61828887	0.81[ASN][1000 genomes]
rs61828888	0.81[ASN][1000 genomes]
rs6425248	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6425249	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6425251	0.87[CEU][hapmap];0.80[CHB][hapmap]
rs6660804	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs6671141	0.85[CHB][hapmap]
rs6675929	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6681766	0.80[CHB][hapmap]
rs6687872	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6699094	1.00[CHB][hapmap]
rs6702320	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72709325	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs728908	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs745573	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs745574	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7520814	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7524592	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs7525100	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs7530469	1.00[CHB][hapmap]
rs7541082	0.87[CEU][hapmap];0.80[CHB][hapmap]
rs7549074	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs898657	0.82[AMR][1000 genomes]
rs898658	0.80[AMR][1000 genomes]
rs898659	0.80[AMR][1000 genomes]
rs912767	1.00[CHB][hapmap];0.84[CHD][hapmap];0.91[JPT][hapmap]

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	nsv872549	chr1:173509586-173546835	Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2422433	PRDX6	cis	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:173523200-173525200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr1:173523200-173525400	Enhancers	HMEC	breast
3	chr1:173523200-173525400	Enhancers	NHEK	skin
4	chr1:173523200-173525600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr1:173523200-173525600	Enhancers	Hela-S3	cervix
6	chr1:173523400-173525400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr1:173523400-173525400	Enhancers	HUVEC	blood vessel
8	chr1:173523600-173529400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr1:173525000-173525400	Enhancers	K562	blood

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