Variant report

Variant	rs12023614
Chromosome Location	chr1:169709274-169709275
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:169708800..169711627-chr1:169714928..169717201,2	MCF-7	breast:
2	chr1:169708422..169710485-chr1:169860930..169862840,2	MCF-7	breast:

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10489181	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10489182	0.93[ASN][1000 genomes]
rs1076637	0.95[CHB][hapmap];0.81[ASN][1000 genomes]
rs10919228	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10919232	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10919233	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11584020	0.83[EUR][1000 genomes]
rs11588380	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12027035	0.95[CHB][hapmap];0.87[MEX][hapmap]
rs12034880	0.82[ASN][1000 genomes]
rs12044082	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12072966	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs12087033	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs16862661	0.88[EUR][1000 genomes]
rs16862663	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16862672	0.84[EUR][1000 genomes]
rs2272818	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2298899	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs2420504	0.88[EUR][1000 genomes]
rs2420505	0.95[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap];0.82[MKK][hapmap];0.93[ASN][1000 genomes]
rs28469136	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs34990593	0.91[ASN][1000 genomes]
rs3917405	0.90[EUR][1000 genomes]
rs3917406	0.91[CHB][hapmap]
rs3917423	0.95[CHB][hapmap]
rs3917428	0.87[CEU][hapmap]
rs3917432	0.87[CEU][hapmap]
rs4656192	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4656699	0.88[EUR][1000 genomes]
rs4656700	0.88[EUR][1000 genomes]
rs4656718	1.00[CEU][hapmap];0.83[TSI][hapmap]
rs4987301	1.00[CEU][hapmap];0.96[TSI][hapmap];0.88[EUR][1000 genomes]
rs4987306	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs4987314	1.00[CEU][hapmap];0.96[TSI][hapmap];0.88[EUR][1000 genomes]
rs4987320	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs4987322	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs4987328	1.00[CEU][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs5356	1.00[CEU][hapmap];0.96[TSI][hapmap];0.90[EUR][1000 genomes]
rs5368	1.00[CEU][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes]
rs57793783	0.84[EUR][1000 genomes]
rs7418242	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs7520701	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7523319	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7523520	0.83[EUR][1000 genomes]
rs7543268	0.93[ASN][1000 genomes]
rs932307	0.91[CHB][hapmap]
rs964555	1.00[CEU][hapmap];0.96[TSI][hapmap];0.87[EUR][1000 genomes]
rs964556	1.00[CEU][hapmap];0.96[TSI][hapmap];0.86[EUR][1000 genomes]
rs964557	1.00[CEU][hapmap];0.96[TSI][hapmap];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532586	chr1:169593222-169713184	Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	esv3451367	chr1:169630075-169976964	Strong transcription Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12023614	C1orf112	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169706400-169710200	Weak transcription	Liver	Liver
2	chr1:169707000-169710200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr1:169707000-169710200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr1:169707000-169710400	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr1:169707200-169710400	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr1:169707400-169710400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr1:169707400-169710600	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr1:169707800-169710400	Enhancers	HUVEC	blood vessel
9	chr1:169708800-169709600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr1:169708800-169713800	Weak transcription	Left Ventricle	heart
11	chr1:169709200-169709400	Flanking Bivalent TSS/Enh	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr1:169709200-169709600	Active TSS	Aorta	Aorta

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