Variant report

Variant	rs1557781
Chromosome Location	chr12:47450220-47450221
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:47448359..47450506-chr12:47463398..47466117,2	MCF-7	breast:
2	chr12:47444845..47446928-chr12:47449328..47451967,2	K562	blood:

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10736030	1.00[CEU][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.96[EUR][1000 genomes]
rs10748457	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10748458	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10748460	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10785649	0.90[ASN][1000 genomes]
rs10785650	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10785653	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10881023	0.89[ASN][1000 genomes]
rs10881024	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10881026	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10881027	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10881029	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10881030	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10881031	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10881033	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1859112	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2158133	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2214335	0.86[EUR][1000 genomes]
rs2408711	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2711698	0.92[EUR][1000 genomes]
rs2711713	0.95[EUR][1000 genomes]
rs7133990	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7136412	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7139043	0.95[EUR][1000 genomes]
rs7311552	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs757149	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs757150	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7956056	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7956758	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7958499	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7961460	1.00[CEU][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7976595	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7978006	0.88[ASN][1000 genomes]
rs7979771	0.90[ASN][1000 genomes]
rs8181633	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs886315	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs886317	0.91[AMR][1000 genomes];0.96[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	nsv469368	chr12:47374908-47675680	Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv558784	chr12:47374908-47675680	Genic enhancers Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1557781	CCNT1	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:47445000-47450400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr12:47447400-47450400	Enhancers	Primary neutrophils fromperipheralblood	blood
3	chr12:47448600-47450600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr12:47450000-47450400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
5	chr12:47450200-47450400	Enhancers	K562	blood

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