Variant report

Variant	rs10916177
Chromosome Location	chr1:227815673-227815674
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10495277	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10799429	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10799438	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1080061	0.94[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs10916172	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1154835	1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs11805477	0.88[ASN][1000 genomes]
rs11806830	0.81[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11807529	0.97[ASN][1000 genomes]
rs12120313	0.98[ASN][1000 genomes]
rs12122398	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12124325	1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs12126339	0.92[ASN][1000 genomes]
rs12131517	0.97[ASN][1000 genomes]
rs12133008	1.00[ASN][1000 genomes]
rs12135976	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12137033	0.98[ASN][1000 genomes]
rs12138942	0.81[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12141938	0.84[ASN][1000 genomes]
rs12408514	0.98[ASN][1000 genomes]
rs1390400	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs16848036	0.88[ASN][1000 genomes]
rs1874371	0.98[ASN][1000 genomes]
rs1923822	1.00[CHB][hapmap];0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs1951729	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2012386	1.00[ASN][1000 genomes]
rs2031134	0.94[ASN][1000 genomes]
rs2093608	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2313245	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2999750	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3010188	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34901559	0.84[ASN][1000 genomes]
rs4306097	0.94[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs4653509	0.81[ASN][1000 genomes]
rs4653851	0.89[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4653862	1.00[ASN][1000 genomes]
rs4653864	0.99[ASN][1000 genomes]
rs4653865	0.86[ASN][1000 genomes]
rs4653867	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs55721361	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55841672	0.88[ASN][1000 genomes]
rs56197655	0.88[ASN][1000 genomes]
rs56349581	0.98[ASN][1000 genomes]
rs57346808	0.96[ASN][1000 genomes]
rs58274339	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59336221	0.86[ASN][1000 genomes]
rs60625678	0.88[ASN][1000 genomes]
rs61322441	0.88[ASN][1000 genomes]
rs61566561	0.94[ASN][1000 genomes]
rs6426469	0.80[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6667937	0.98[ASN][1000 genomes]
rs6699448	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7528010	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9725624	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	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
3	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
4	esv3327012	chr1:227741102-227890968	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	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
6	nsv945673	chr1:227799341-227819395	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10916177	ZNF678	cis	normal skin	skin_eQTL
rs10916177	ZNF678	Cis_1M	lymphoblastoid	RTeQTL
rs10916177	ZNF678	cis	lesional skin	skin_eQTL
rs10916177	ZNF678	cis	uninvolved skin	skin_eQTL

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227770000-227853800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr1:227790400-227834800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr1:227800200-227820600	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr1:227801200-227821800	Weak transcription	Stomach Smooth Muscle	stomach
5	chr1:227805800-227823600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr1:227811800-227830600	ZNF genes & repeats	Liver	Liver
7	chr1:227812400-227816400	Weak transcription	Psoas Muscle	Psoas
8	chr1:227814600-227815800	Weak transcription	Fetal Lung	lung
9	chr1:227815200-227819200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr1:227815200-227828800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr1:227815400-227815800	ZNF genes & repeats	Fetal Muscle Leg	muscle
12	chr1:227815400-227820800	Weak transcription	Ovary	ovary

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