Variant report

Variant	rs4768875
Chromosome Location	chr12:51428089-51428090
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:51422433..51425067-chr12:51426862..51428458,2	MCF-7	breast:

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10783411	0.82[AFR][1000 genomes]
rs10876126	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1095997	0.95[AMR][1000 genomes]
rs11169679	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12423207	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12814178	0.81[AFR][1000 genomes]
rs150909	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs161044	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs161045	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs161046	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs161047	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17229232	0.80[EUR][1000 genomes]
rs2029147	0.80[EUR][1000 genomes]
rs2046498	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs224564	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs224566	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs224569	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs224570	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs224573	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs224574	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs224576	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs224578	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs224585	0.91[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs224586	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs224590	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs224592	0.96[EUR][1000 genomes]
rs224593	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2554858	0.86[AMR][1000 genomes]
rs2554859	0.90[AMR][1000 genomes]
rs2554861	0.83[AMR][1000 genomes]
rs2630353	0.83[AMR][1000 genomes]
rs2630358	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2630362	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2630366	1.00[AMR][1000 genomes]
rs2630367	1.00[AMR][1000 genomes]
rs319930	1.00[AMR][1000 genomes]
rs319938	1.00[AMR][1000 genomes]
rs319941	0.83[AMR][1000 genomes]
rs319943	0.83[AMR][1000 genomes]
rs319944	0.83[AMR][1000 genomes]
rs364627	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs390424	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs394384	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs416062	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4238110	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs435965	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs445520	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs452587	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4768959	0.82[AFR][1000 genomes]
rs55874852	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs613977	0.98[EUR][1000 genomes]
rs618510	0.92[EUR][1000 genomes]
rs6580779	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6580780	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6580781	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6580783	0.83[AFR][1000 genomes]
rs686528	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs706803	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs706804	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7299484	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7968372	0.80[EUR][1000 genomes]
rs7969536	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7969702	0.92[EUR][1000 genomes]
rs7971712	0.92[EUR][1000 genomes]
rs7972608	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7974923	0.85[AFR][1000 genomes]
rs7975117	0.86[AMR][1000 genomes]
rs7975628	0.85[AFR][1000 genomes]
rs829016	0.83[AMR][1000 genomes]
rs829021	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs853236	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9739943	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[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
rs4768875	SLC11A2	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51422800-51432000	Weak transcription	Stomach Mucosa	stomach
2	chr12:51423800-51431800	Weak transcription	Hela-S3	cervix
3	chr12:51426400-51428400	Enhancers	K562	blood
4	chr12:51427600-51429200	Weak transcription	HepG2	liver

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