Variant report

Variant	rs4667667
Chromosome Location	chr2:171779154-171779155
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 88 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10198197	0.83[CEU][hapmap]
rs10208341	0.83[CEU][hapmap]
rs10210883	0.82[CEU][hapmap]
rs1035825	0.82[CEU][hapmap]
rs1035827	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs10803853	0.83[EUR][1000 genomes]
rs10803854	0.87[CEU][hapmap]
rs10930449	0.87[CEU][hapmap]
rs10930453	0.83[CEU][hapmap]
rs10930455	0.83[CEU][hapmap]
rs10930456	0.83[CEU][hapmap]
rs10930457	0.83[CEU][hapmap]
rs11686985	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11696064	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs11902360	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11902369	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[AFR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11904750	0.86[CHB][hapmap]
rs12467411	0.82[CHB][hapmap]
rs12473741	0.86[CHB][hapmap]
rs12477649	0.86[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs12612871	0.86[CEU][hapmap];0.81[YRI][hapmap]
rs12618898	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs12621769	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13004273	0.82[CEU][hapmap]
rs13010307	0.83[CEU][hapmap]
rs13025033	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13030784	0.83[CEU][hapmap]
rs13036123	0.81[CEU][hapmap]
rs13410683	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs13411575	0.82[CEU][hapmap]
rs13425247	0.83[CEU][hapmap]
rs1529378	0.82[CEU][hapmap]
rs1529391	0.82[CEU][hapmap]
rs16859050	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16859157	0.83[CHB][hapmap]
rs17505447	0.83[CHB][hapmap]
rs1978592	0.82[CEU][hapmap]
rs2059723	0.86[CHB][hapmap]
rs2081767	0.86[CHB][hapmap]
rs2081768	0.86[CHB][hapmap]
rs2098999	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2195116	0.95[CEU][hapmap];0.93[EUR][1000 genomes]
rs2356422	0.87[CHB][hapmap]
rs2555922	0.83[CEU][hapmap]
rs2557794	0.82[CEU][hapmap]
rs2676151	0.82[CEU][hapmap]
rs3731993	0.83[CHB][hapmap]
rs3755121	0.82[CEU][hapmap]
rs3755124	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3755126	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3770423	0.83[CEU][hapmap]
rs3770428	0.83[CEU][hapmap]
rs3770433	0.83[CEU][hapmap]
rs3770436	0.81[CHB][hapmap]
rs3770438	0.91[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.81[YRI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4667673	0.87[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs4668343	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4668344	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4668345	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4668346	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4668354	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4668355	0.87[CEU][hapmap]
rs6433264	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6433266	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6433267	0.82[EUR][1000 genomes]
rs6433276	0.82[CEU][hapmap]
rs6714164	0.82[CEU][hapmap]
rs6729847	0.81[EUR][1000 genomes]
rs6730417	0.82[CEU][hapmap]
rs6731774	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6733178	0.82[CEU][hapmap]
rs6742564	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6742797	0.87[CEU][hapmap]
rs6754315	0.85[CEU][hapmap]
rs6760293	0.81[AMR][1000 genomes]
rs6761642	0.82[CEU][hapmap]
rs731693	0.87[CEU][hapmap]
rs754058	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs7559136	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7560889	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7567927	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7585607	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7598194	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7606822	0.81[CEU][hapmap]
rs930035	0.86[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs930036	0.86[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs964172	0.86[CEU][hapmap];0.95[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4667667	TLK1	cis	lesional skin	skin_eQTL
rs4667667	TLK1	cis	normal skin	skin_eQTL
rs4667667	TLK1	Cis_1M	lymphoblastoid	RTeQTL
rs4667667	TLK1	cis	uninvolved skin	skin_eQTL

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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