Variant report

Variant	rs12124325
Chromosome Location	chr1:227913256-227913257
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:227910908-227920562	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr1:227913000-227913345	HepG2	liver:	n/a	n/a
3	POLR2A	chr1:227910941-227920625	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:227912232..227914345-chr1:228021397..228023530,2	K562	blood:
2	chr1:227707174..227709408-chr1:227913007..227914780,2	K562	blood:
3	chr1:227899761..227902158-chr1:227912369..227914847,2	K562	blood:
4	chr1:227907636..227909254-chr1:227910705..227913519,2	K562	blood:
5	chr1:227906153..227908527-chr1:227912474..227914252,2	K562	blood:
6	chr1:227821457..227823471-chr1:227912921..227914771,2	K562	blood:
7	chr1:227912717..227914505-chr1:228107009..228109578,2	K562	blood:

No data

Variant related genes	Relation type
SNAP47	TF binding region
ENSG00000227711	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10495277	0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10799429	0.83[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10799438	1.00[CEU][hapmap];0.89[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10916172	1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs10916177	1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs1154835	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11805477	0.91[CEU][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11806830	1.00[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11807529	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12120313	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12122398	0.91[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12123869	0.81[EUR][1000 genomes]
rs12126339	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12131517	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12133008	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12135976	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12137033	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12138942	0.90[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12141938	0.89[CEU][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12408514	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1390400	0.90[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16848036	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1874371	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1923822	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1951729	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2012386	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2031134	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2093608	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2313245	0.91[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2999750	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3010188	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3087908	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34901559	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4306097	0.91[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap]
rs4653851	0.91[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4653862	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4653864	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4653865	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4653867	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs55721361	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[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];0.84[ASN][1000 genomes]
rs57346808	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58274339	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[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];0.91[ASN][1000 genomes]
rs6426469	1.00[CEU][hapmap];0.80[CHB][hapmap];0.89[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6667937	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6699448	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs751748	0.90[CEU][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];0.84[ASN][1000 genomes]
rs9725624	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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
rs12124325	ZNF678	cis	uninvolved skin	skin_eQTL
rs12124325	ZNF678	cis	normal skin	skin_eQTL
rs12124325	ZNF678	Cis_1M	lymphoblastoid	RTeQTL
rs12124325	ZNF678	cis	lesional skin	skin_eQTL

Chromatin state (count:3 , 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	chr1:227912200-227913400	Enhancers	Fetal Muscle Leg	muscle
3	chr1:227912600-227913400	Enhancers	HSMMtube	muscle

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