Variant report

Variant	rs1255742
Chromosome Location	chr14:64030046-64030047
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	E2F4	chr14:64029897-64030047	MCF10A-Er-Src	breast:	n/a	n/a
2	GATA3	chr14:64030031-64030794	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:64028657..64030519-chr14:64106654..64108716,2	MCF-7	breast:
2	chr14:64009657..64011362-chr14:64029023..64031031,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000205767	TF binding region
ENSG00000154001	Chromatin interaction
ENSG00000261242	Chromatin interaction
ENSG00000140006	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1152449	0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs12232206	0.86[ASN][1000 genomes]
rs1255639	0.88[MEX][hapmap];0.81[TSI][hapmap]
rs1255718	0.92[ASW][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.91[MKK][hapmap];0.83[TSI][hapmap];0.84[YRI][hapmap];0.82[ASN][1000 genomes]
rs1255721	0.92[ASW][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.85[MKK][hapmap];0.83[TSI][hapmap];0.82[ASN][1000 genomes]
rs1255722	0.83[ASW][hapmap];0.81[TSI][hapmap]
rs1255723	0.81[ASN][1000 genomes]
rs1255733	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1255737	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1255739	1.00[CEU][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1255741	0.91[ASW][hapmap];1.00[CEU][hapmap];0.80[CHB][hapmap];0.89[GIH][hapmap];0.88[MEX][hapmap];0.80[MKK][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1255743	0.96[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1255746	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1255777	0.82[ASN][1000 genomes]
rs1255788	0.83[ASN][1000 genomes]
rs1271563	0.92[ASW][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.91[MKK][hapmap];0.83[TSI][hapmap];0.84[YRI][hapmap];0.82[ASN][1000 genomes]
rs2754223	1.00[ASW][hapmap];0.81[CHD][hapmap];0.88[MEX][hapmap];0.81[TSI][hapmap];0.91[YRI][hapmap]
rs6573522	0.88[MEX][hapmap];0.81[TSI][hapmap]
rs7143992	0.84[ASN][1000 genomes]
rs964954	0.92[ASW][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap];0.80[MKK][hapmap];0.83[TSI][hapmap];0.81[ASN][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	nsv527251	chr14:63400786-64068806	Flanking Bivalent TSS/Enh Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv520528	chr14:63400786-64157117	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv915909	chr14:63620440-64560369	Active TSS Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
4	nsv974442	chr14:64024425-64046914	Enhancers Weak transcription Bivalent Enhancer	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1255742	PRKCH	cis	parietal	SCAN
rs1255742	SIX6	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:64027600-64030200	Weak transcription	Placenta	Placenta
2	chr14:64029200-64032400	Enhancers	Hela-S3	cervix
3	chr14:64029400-64031600	Enhancers	HMEC	breast
4	chr14:64029800-64031400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr14:64030000-64031000	Weak transcription	A549	lung
6	chr14:64030000-64031200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr14:64030000-64031200	Enhancers	NHEK	skin
8	chr14:64030000-64031400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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