Variant report

Variant	rs4653867
Chromosome Location	chr1:227914867-227914868
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10495277	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10799429	0.85[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10799438	1.00[CEU][hapmap];0.89[JPT][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10916172	1.00[CHB][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs10916177	1.00[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs1154835	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11805477	0.92[CEU][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11806830	1.00[CEU][hapmap];0.80[CHB][hapmap];0.89[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11807529	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12120313	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12122398	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];0.84[MEX][hapmap];0.81[TSI][hapmap];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12123869	0.81[EUR][1000 genomes]
rs12124325	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12126339	0.80[EUR][1000 genomes]
rs12131517	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12133008	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12135976	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12137033	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12138942	0.91[CEU][hapmap];0.80[CHB][hapmap];0.89[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12141938	0.91[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12408514	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1390400	0.91[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16848036	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1874371	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1923822	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1951729	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2012386	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2031134	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2093608	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2313245	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];0.84[MEX][hapmap];0.81[TSI][hapmap];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2999750	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3010188	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3087908	0.83[TSI][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34901559	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4306097	0.92[CEU][hapmap];0.94[CHB][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];0.84[JPT][hapmap];0.94[MEX][hapmap]
rs4653851	0.92[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.80[EUR][1000 genomes]
rs4653862	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4653864	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4653865	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55721361	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55841672	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56197655	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56349581	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs57346808	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs58274339	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59336221	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs60625678	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61322441	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61566561	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6426469	1.00[CEU][hapmap];0.80[CHB][hapmap];0.89[JPT][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6667937	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6699448	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs751748	0.91[CEU][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7528010	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs754224	0.88[MEX][hapmap];0.81[TSI][hapmap]
rs9725624	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[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	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
3	nsv1010605	chr1:227770415-228332690	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
4	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
5	nsv427952	chr1:227881664-228308629	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
6	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
7	nsv945344	chr1:227899939-227917776	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
8	nsv515496	chr1:227912474-227967938	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4653867	ZNF678	cis	normal skin	skin_eQTL
rs4653867	ZNF678	Cis_1M	lymphoblastoid	RTeQTL
rs4653867	ZNF678	cis	uninvolved skin	skin_eQTL
rs4653867	ZNF678	cis	lesional skin	skin_eQTL

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227911400-227915600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr1:227913400-227915600	Weak transcription	HSMMtube	muscle
3	chr1:227914400-227915200	ZNF genes & repeats	GM12878-XiMat	blood
4	chr1:227914600-227915200	Enhancers	Hela-S3	cervix

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