Variant report

Variant	rs162473
Chromosome Location	chr5:98140980-98140981
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:98134722..98137912-chr5:98138066..98142430,3	MCF-7	breast:

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1069182	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs150991	0.82[EUR][1000 genomes]
rs161735	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs161740	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs161747	0.81[EUR][1000 genomes]
rs161933	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs161938	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs161939	0.84[EUR][1000 genomes]
rs161941	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs161942	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs161950	0.80[EUR][1000 genomes]
rs161951	0.80[EUR][1000 genomes]
rs161952	0.81[EUR][1000 genomes]
rs161953	0.82[EUR][1000 genomes]
rs161954	0.86[EUR][1000 genomes]
rs162140	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs162149	0.87[EUR][1000 genomes]
rs162150	0.87[EUR][1000 genomes]
rs162611	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs170734	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs193072	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2545729	0.85[ASN][1000 genomes]
rs2617507	0.81[EUR][1000 genomes]
rs2617512	0.85[ASN][1000 genomes]
rs2662259	0.85[ASN][1000 genomes]
rs2662261	0.85[ASN][1000 genomes]
rs325217	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs326463	0.82[EUR][1000 genomes]
rs326464	0.87[EUR][1000 genomes]
rs326468	0.87[EUR][1000 genomes]
rs326469	0.83[EUR][1000 genomes]
rs326485	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs326489	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs327792	0.82[EUR][1000 genomes]
rs327803	0.81[EUR][1000 genomes]
rs330419	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs330421	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs330422	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs331543	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs331545	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs331549	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs331918	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs331926	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs331929	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs331930	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs331931	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs466340	0.82[EUR][1000 genomes]
rs692832	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs751878	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs992773	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs992775	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][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	nsv882414	chr5:98063710-98193164	Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv882415	chr5:98134186-98312447	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs162473	RGMB	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:98129400-98141200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr5:98131200-98141400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr5:98132600-98142200	Weak transcription	NHLF	lung
4	chr5:98132600-98154000	Weak transcription	HSMM	muscle
5	chr5:98140400-98142200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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