Variant report

Variant	rs278917
Chromosome Location	chr12:41380488-41380489
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:41379403..41382000-chr19:56843629..56845735,2	MCF-7	breast:

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1056019	0.84[ASN][1000 genomes]
rs10784967	0.86[ASN][1000 genomes]
rs10879401	0.86[ASN][1000 genomes]
rs10879420	0.87[ASN][1000 genomes]
rs10879442	0.93[ASW][hapmap];0.84[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.90[LWK][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10879443	0.84[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.82[YRI][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1372539	0.83[ASN][1000 genomes]
rs1372541	0.83[ASN][1000 genomes]
rs1442193	0.83[ASN][1000 genomes]
rs1470210	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1946969	0.86[ASN][1000 genomes]
rs278915	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs278916	0.93[AFR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34169502	0.84[ASN][1000 genomes]
rs443310	0.93[AFR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4768319	0.86[CHD][hapmap]
rs6582087	0.83[ASN][1000 genomes]
rs712132	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs712133	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs712134	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs712137	0.90[AFR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7303364	0.80[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs7311097	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7979570	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs880180	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs935101	0.85[EUR][1000 genomes];0.89[ASN][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	nsv497867	chr12:41286305-41728650	Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv832382	chr12:41359550-41489681	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv1042296	chr12:41372512-41401840	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
4	nsv427910	chr12:41374913-41650593	Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv428587	chr12:41375635-41546845	Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Active TSS Active TSS 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
rs278917	YAF2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:41374600-41404800	Weak transcription	Brain Angular Gyrus	brain
2	chr12:41374800-41386200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr12:41377400-41386200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr12:41379800-41381200	Weak transcription	Colon Smooth Muscle	Colon

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