Variant report

Variant	rs12029431
Chromosome Location	chr1:152391547-152391548
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr1:152391382-152391674	T-47D	breast:	n/a	n/a
2	FOXA1	chr1:152391379-152391591	T-47D	breast:	n/a	n/a
3	FOXA1	chr1:152391334-152391602	T-47D	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:152385310..152387718-chr1:152390033..152392534,2	MCF-7	breast:

Variant related genes	Relation type
CRNN	TF binding region
ENSG00000143536	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10888486	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11204982	0.81[JPT][hapmap]
rs11204985	0.81[JPT][hapmap]
rs11204986	0.81[JPT][hapmap];0.84[AMR][1000 genomes]
rs11205001	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11301808	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11583558	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11588022	0.83[AMR][1000 genomes]
rs11590822	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12024486	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12048587	0.83[ASN][1000 genomes]
rs12049036	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12403031	0.85[JPT][hapmap];0.84[AMR][1000 genomes]
rs12408401	0.85[CEU][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12568784	0.81[JPT][hapmap]
rs1923491	0.92[CHB][hapmap];0.83[ASN][1000 genomes]
rs1923493	1.00[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1923505	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1923509	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2065954	0.81[JPT][hapmap]
rs2146117	0.83[CEU][hapmap];1.00[YRI][hapmap]
rs2146121	0.90[ASN][1000 genomes]
rs3753443	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3753444	1.00[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3753446	0.83[ASN][1000 genomes]
rs3829868	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4285700	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4378206	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs45541239	0.84[AMR][1000 genomes]
rs4845766	0.92[CHB][hapmap];0.83[JPT][hapmap];0.90[ASN][1000 genomes]
rs6587668	0.84[AMR][1000 genomes]
rs6679449	0.81[JPT][hapmap]
rs6679899	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6693160	0.84[AMR][1000 genomes]
rs6696556	0.83[CEU][hapmap]
rs726863	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs726865	0.84[ASN][1000 genomes]
rs7515448	0.81[JPT][hapmap]
rs7521839	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9633410	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12029431	CRNN	cis	Esophagus Mucosa	GTEx

Chromatin state (count:0 , 50 per page) page:

No data

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