Variant report

Variant	rs12024486
Chromosome Location	chr1:152381085-152381086
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:152379306..152381264-chr1:152411990..152414045,3	MCF-7	breast:
2	chr1:152376781..152379524-chr1:152379783..152382787,3	MCF-7	breast:
3	chr1:152379125..152381578-chr1:152431090..152434005,2	MCF-7	breast:
4	chr1:152370276..152371967-chr1:152379083..152381253,2	MCF-7	breast:

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10888486	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11204985	0.81[EUR][1000 genomes]
rs11204986	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11204987	0.81[EUR][1000 genomes]
rs11205001	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11301808	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11583558	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11588022	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11590822	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12022217	0.81[EUR][1000 genomes]
rs12027445	0.81[EUR][1000 genomes]
rs12029431	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12048587	0.84[ASN][1000 genomes]
rs12049036	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12403031	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12408401	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12568784	0.81[EUR][1000 genomes]
rs1858485	0.81[EUR][1000 genomes]
rs1923491	0.84[ASN][1000 genomes]
rs1923493	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1923505	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1923509	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2065954	0.81[EUR][1000 genomes]
rs2146121	0.85[ASN][1000 genomes]
rs2525	0.81[EUR][1000 genomes]
rs3120666	0.81[EUR][1000 genomes]
rs3753443	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3753444	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3753446	0.84[ASN][1000 genomes]
rs3829868	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4285700	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4378206	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs45541239	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4845766	0.85[ASN][1000 genomes]
rs6587668	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6679899	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6693160	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs726863	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7521839	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs941935	0.81[EUR][1000 genomes]
rs9633410	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014095	chr1:152104486-152454591	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv1005472	chr1:152247763-152443448	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv535161	chr1:152247763-152443448	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv916016	chr1:152337775-152590520	Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv516541	chr1:152376710-152390452	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12024486	CRNN	cis	Esophagus Mucosa	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:152378000-152382000	Weak transcription	Esophagus	oesophagus
2	chr1:152378800-152382400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr1:152380600-152383000	Weak transcription	Fetal Lung	lung
4	chr1:152381000-152385800	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell

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