Variant report

Variant	rs6724493
Chromosome Location	chr2:171779109-171779110
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 120 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:119)

rs_ID	r²[population]
rs10189480	0.95[CEU][hapmap];1.00[CHB][hapmap]
rs10198197	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10207361	1.00[CHB][hapmap]
rs10208341	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10210883	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1025240	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1035825	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1035826	0.95[CEU][hapmap];1.00[CHB][hapmap]
rs1035828	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1045327	0.95[CEU][hapmap];1.00[CHB][hapmap]
rs10515934	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10803853	1.00[ASN][1000 genomes]
rs10803854	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10930448	0.94[ASN][1000 genomes]
rs10930449	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10930453	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10930455	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10930456	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10930457	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12151587	0.81[ASN][1000 genomes]
rs12471930	0.94[ASN][1000 genomes]
rs12612871	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12988738	0.83[ASN][1000 genomes]
rs12996518	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12997252	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12998296	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13000898	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs13001088	0.81[AMR][1000 genomes]
rs13002517	0.95[CEU][hapmap];1.00[CHB][hapmap]
rs13003218	0.95[CEU][hapmap];1.00[CHB][hapmap]
rs13004273	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13010307	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13011011	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13015226	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13016705	1.00[CHB][hapmap]
rs13026662	0.88[ASN][1000 genomes]
rs13028857	0.80[EUR][1000 genomes]
rs13030784	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13035460	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13036123	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13402107	1.00[CHB][hapmap]
rs13411575	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13425247	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13427723	1.00[CHB][hapmap]
rs1529378	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1529391	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs16859066	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16859081	0.85[ASN][1000 genomes]
rs17281735	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1978592	1.00[JPT][hapmap]
rs1991370	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2033160	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2052808	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2114738	0.88[ASN][1000 genomes]
rs2195116	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2555922	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2557794	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2557799	0.88[ASN][1000 genomes]
rs2676131	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2676151	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2723241	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs34004615	0.85[ASN][1000 genomes]
rs34017170	0.85[ASN][1000 genomes]
rs34330182	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34342928	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34532258	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34911788	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35123411	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35230775	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35864840	0.85[ASN][1000 genomes]
rs35890547	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35987434	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3755121	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3755125	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3770423	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3770428	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3770433	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3770435	0.80[ASN][1000 genomes]
rs3770440	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3770441	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3770442	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3821090	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4668349	0.84[ASN][1000 genomes]
rs4668350	0.84[ASN][1000 genomes]
rs4668355	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4668368	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs5028603	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6433267	1.00[ASN][1000 genomes]
rs6433276	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6709077	0.85[ASN][1000 genomes]
rs6714164	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6714300	0.94[ASN][1000 genomes]
rs6715386	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6729847	1.00[ASN][1000 genomes]
rs6730417	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6733178	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6734903	0.85[ASN][1000 genomes]
rs6742797	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6743201	0.85[ASN][1000 genomes]
rs6754315	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6758331	0.90[CEU][hapmap];1.00[CHB][hapmap]
rs6761642	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6761759	0.95[CEU][hapmap];1.00[CHB][hapmap]
rs6761889	0.95[CEU][hapmap];1.00[CHB][hapmap]
rs71415229	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71415231	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs71415232	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs71415233	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs731692	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[YRI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs731693	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs73976229	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7560889	0.82[EUR][1000 genomes]
rs7570701	0.94[ASN][1000 genomes]
rs7580629	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7587244	0.95[CEU][hapmap];1.00[CHB][hapmap]
rs7593193	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7606822	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs960222	0.81[ASN][1000 genomes]
rs965518	0.88[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	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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6724493	TLK1	cis	normal skin	skin_eQTL
rs6724493	TLK1	cis	uninvolved skin	skin_eQTL
rs6724493	TLK1	cis	lesional skin	skin_eQTL
rs6724493	TLK1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:171774600-171779800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr2:171774800-171779400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr2:171775000-171784800	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr2:171775400-171779600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr2:171776000-171779400	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr2:171778000-171779600	Enhancers	HepG2	liver
7	chr2:171778200-171784800	Weak transcription	Right Ventricle	heart
8	chr2:171778400-171785000	Weak transcription	Right Atrium	heart
9	chr2:171778600-171780000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr2:171779000-171784600	Weak transcription	Fetal Heart	heart

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