Variant report

Variant	rs206952
Chromosome Location	chr12:120823722-120823723
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:120806059..120810097-chr12:120821130..120825339,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135097	Chromatin interaction
ENSG00000239881	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1076206	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1179430	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1179433	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1179434	0.83[CHB][hapmap]
rs1179436	0.88[EUR][1000 genomes]
rs1179437	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1179438	1.00[ASW][hapmap];0.91[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];0.86[GIH][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.81[YRI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1179440	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1179441	0.91[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];0.86[GIH][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1179442	0.91[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];0.86[GIH][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1179443	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1179445	0.91[CEU][hapmap];0.91[CHB][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1179446	0.91[CEU][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];0.86[GIH][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap];0.81[YRI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1179447	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1179449	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1179451	0.85[ASN][1000 genomes]
rs1183783	0.85[JPT][hapmap]
rs1184532	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12298898	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1306624	0.91[CEU][hapmap];0.91[CHB][hapmap];0.84[EUR][1000 genomes]
rs206948	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs206949	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs206950	0.87[CEU][hapmap];0.84[TSI][hapmap]
rs2261612	0.86[ASW][hapmap];0.82[CEU][hapmap];0.89[TSI][hapmap]
rs2283367	0.83[ASN][1000 genomes]
rs2285679	0.91[CHB][hapmap];0.84[CHD][hapmap]
rs2522133	0.82[CEU][hapmap]
rs2522134	0.88[ASW][hapmap];0.82[CEU][hapmap];0.91[TSI][hapmap];0.80[EUR][1000 genomes]
rs2859287	0.87[CEU][hapmap];0.82[TSI][hapmap]
rs2951690	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3782901	0.91[CHB][hapmap];0.81[CHD][hapmap];0.83[ASN][1000 genomes]
rs4767890	0.97[ASN][1000 genomes]
rs735382	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs757122	0.91[CEU][hapmap];0.91[CHB][hapmap];0.81[YRI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs916842	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899555	chr12:120519124-120840522	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	499 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs206952	FBXO21	cis	parietal	SCAN
rs206952	POP5	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:120815600-120825800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr12:120820400-120826600	Weak transcription	Ovary	ovary
3	chr12:120820400-120826800	Weak transcription	Right Atrium	heart
4	chr12:120821000-120826400	Weak transcription	Fetal Intestine Small	intestine

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