Variant report

Variant	rs1080061
Chromosome Location	chr1:227709997-227709998
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	WRNIP1	chr1:227709990-227710158	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000227711	TF binding region

Extended variants
information (count: 49 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10495277	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10799429	0.92[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10799438	0.92[CEU][hapmap];0.94[JPT][hapmap]
rs10916172	0.94[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs10916177	0.94[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs1154835	0.92[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap]
rs11805477	0.84[CEU][hapmap]
rs11806830	0.92[CEU][hapmap];0.95[JPT][hapmap]
rs11807529	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12120313	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12122398	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12126339	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12131517	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12133008	0.82[ASN][1000 genomes]
rs12135976	0.82[ASN][1000 genomes]
rs12137033	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12138942	0.84[CEU][hapmap];0.95[JPT][hapmap]
rs12408514	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1390400	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1874371	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1923822	0.92[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap]
rs1951729	0.92[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs2012386	0.82[ASN][1000 genomes]
rs2031134	0.80[AMR][1000 genomes]
rs2093608	0.89[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs2313245	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2999750	0.80[ASN][1000 genomes]
rs3010188	0.82[ASN][1000 genomes]
rs4306097	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4653509	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4653851	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4653862	0.82[ASN][1000 genomes]
rs4653864	0.81[ASN][1000 genomes]
rs55721361	0.82[ASN][1000 genomes]
rs56349581	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs58274339	0.82[ASN][1000 genomes]
rs61566561	0.80[AMR][1000 genomes]
rs6426469	0.92[CEU][hapmap];0.95[JPT][hapmap]
rs6667937	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6699448	0.82[ASN][1000 genomes]
rs7528010	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
2	esv2753828	chr1:227670265-227791265	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv945337	chr1:227680551-227712483	ZNF genes & repeats Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv873244	chr1:227682414-227736363	Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv873246	chr1:227694948-227884465	Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1007479	chr1:227695868-227984466	Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
7	nsv873247	chr1:227697381-227736363	Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv947072	chr1:227709512-227712483	Enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1080061	ZNF678	cis	lesional skin	skin_eQTL
rs1080061	ZNF678	Cis_1M	lymphoblastoid	RTeQTL
rs1080061	ZNF678	cis	uninvolved skin	skin_eQTL
rs1080061	ZNF678	cis	normal skin	skin_eQTL

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227709200-227710200	Enhancers	HSMMtube	muscle
2	chr1:227709600-227710200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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