Variant report

Variant	rs6580781
Chromosome Location	chr12:51433281-51433282
allele	C/T
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
ENSG00000110925	Chromatin interaction
ENSG00000050426	Chromatin interaction
ENSG00000110911	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10876126	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11169679	0.90[EUR][1000 genomes]
rs12423207	0.90[EUR][1000 genomes]
rs150909	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs161044	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs161045	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs161046	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs161047	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs224564	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs224566	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs224569	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs224570	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs224573	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs224574	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs224578	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs224585	0.85[EUR][1000 genomes]
rs224586	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs224590	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs224592	0.87[EUR][1000 genomes]
rs224593	0.87[EUR][1000 genomes]
rs2630358	0.80[AMR][1000 genomes]
rs2630362	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2630366	0.80[AMR][1000 genomes]
rs2630367	0.80[AMR][1000 genomes]
rs319930	0.80[AMR][1000 genomes]
rs319938	0.80[AMR][1000 genomes]
rs364627	0.90[EUR][1000 genomes]
rs390424	0.87[EUR][1000 genomes]
rs394384	0.83[EUR][1000 genomes]
rs416062	0.90[EUR][1000 genomes]
rs4238110	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs435965	0.90[EUR][1000 genomes]
rs445520	0.87[EUR][1000 genomes]
rs452587	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4768875	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55874852	0.80[AMR][1000 genomes]
rs613977	0.89[EUR][1000 genomes]
rs618510	0.87[EUR][1000 genomes]
rs6580779	0.85[EUR][1000 genomes]
rs6580780	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs686528	0.90[EUR][1000 genomes]
rs706803	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs706804	0.81[EUR][1000 genomes]
rs7299484	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7969536	0.89[EUR][1000 genomes]
rs7969702	0.83[EUR][1000 genomes]
rs7971712	0.83[EUR][1000 genomes]
rs829021	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs853236	0.80[AMR][1000 genomes]
rs9739943	0.83[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	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
rs6580781	SLC11A2	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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