Variant report

Variant	rs55679918
Chromosome Location	chr12:51433276-51433277
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:51417280..51420839-chr12:51432124..51433925,3	MCF-7	breast:
2	chr12:51432107..51434047-chr12:51440575..51442200,2	MCF-7	breast:
3	chr12:51432148..51434045-chr12:51470085..51473037,2	K562	blood:

Variant related genes	Relation type
ENSG00000050426	Chromatin interaction
ENSG00000110911	Chromatin interaction
ENSG00000110925	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1079521	0.87[AMR][1000 genomes]
rs12580097	0.84[EUR][1000 genomes]
rs12582592	0.84[EUR][1000 genomes]
rs17125258	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17125286	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17125346	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17125369	0.84[EUR][1000 genomes]
rs17125375	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17125401	0.81[EUR][1000 genomes]
rs224446	0.82[AMR][1000 genomes]
rs224454	0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs224568	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs224587	0.82[AMR][1000 genomes]
rs2269684	0.91[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2269685	0.87[AMR][1000 genomes]
rs2269686	0.82[AMR][1000 genomes]
rs3759406	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs453313	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4768869	0.84[AMR][1000 genomes]
rs4768876	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55864652	0.82[EUR][1000 genomes]
rs55871024	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs55897461	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs55987825	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56060103	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56335028	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56353532	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56847302	0.84[EUR][1000 genomes]
rs60910794	0.84[EUR][1000 genomes]
rs61005916	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs67466786	0.84[EUR][1000 genomes]
rs73090660	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73090661	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73092534	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73103154	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73105025	0.84[EUR][1000 genomes]
rs7397054	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7397068	0.82[AMR][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	esv3414501	chr12:51174503-51534707	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	esv34039	chr12:51326702-51671911	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs55679918	TFCP2	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51430400-51434800	Weak transcription	Fetal Intestine Large	intestine
2	chr12:51431800-51434000	Enhancers	Hela-S3	cervix
3	chr12:51432000-51434000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr12:51432600-51434800	Weak transcription	HepG2	liver
5	chr12:51432800-51434200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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