Variant report

Variant	rs7560889
Chromosome Location	chr2:171762882-171762883
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1035827	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs11686985	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11696064	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs11902360	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11902369	0.91[CHB][hapmap];0.96[JPT][hapmap];0.85[AFR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11904750	0.81[CHB][hapmap]
rs12473741	0.81[CHB][hapmap]
rs12477649	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs12612871	0.81[YRI][hapmap]
rs12618898	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs12621769	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13015226	0.83[EUR][1000 genomes]
rs13025033	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13035460	0.82[EUR][1000 genomes]
rs16859050	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2059723	0.81[CHB][hapmap]
rs2081767	0.81[CHB][hapmap]
rs2081768	0.82[CHB][hapmap]
rs2098999	0.81[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2195116	0.81[EUR][1000 genomes]
rs2356422	0.82[CHB][hapmap]
rs34532258	0.82[EUR][1000 genomes]
rs35230775	0.83[EUR][1000 genomes]
rs3755124	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3755125	0.82[EUR][1000 genomes]
rs3755126	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3770438	0.86[CHB][hapmap];0.90[JPT][hapmap];0.81[YRI][hapmap]
rs4667667	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4667673	0.87[CHB][hapmap];0.96[JPT][hapmap]
rs4668343	0.81[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4668344	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4668345	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4668346	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4668354	0.96[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6433264	0.86[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs6433266	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6715386	0.81[EUR][1000 genomes]
rs6724493	0.82[EUR][1000 genomes]
rs6731774	0.81[ASN][1000 genomes]
rs6742564	0.82[ASN][1000 genomes]
rs71415229	0.83[EUR][1000 genomes]
rs754058	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs7559136	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7567927	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7585607	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7598194	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs930035	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs930036	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs964172	0.91[CHB][hapmap];1.00[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	nsv431801	chr2:171721493-171966493	ZNF genes & repeats Strong transcription Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7560889	TLK1	cis	normal skin	skin_eQTL
rs7560889	TLK1	cis	lesional skin	skin_eQTL
rs7560889	TLK1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:171762600-171771600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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