Variant report

Variant	rs331930
Chromosome Location	chr5:98169263-98169264
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RGMB-4	chr5:98169086-98169415	NONHSAT102959

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10040066	0.82[CEU][hapmap]
rs1069182	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1472622	0.82[CEU][hapmap]
rs150991	0.84[EUR][1000 genomes]
rs161735	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs161740	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs161747	0.83[EUR][1000 genomes]
rs161933	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs161935	0.85[CEU][hapmap]
rs161936	0.92[CEU][hapmap]
rs161938	0.82[CEU][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs161939	0.86[EUR][1000 genomes]
rs161941	0.92[CEU][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs161942	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs161950	0.83[EUR][1000 genomes]
rs161951	0.83[EUR][1000 genomes]
rs161952	0.87[YRI][hapmap];0.83[EUR][1000 genomes]
rs161953	0.84[EUR][1000 genomes]
rs161954	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs161956	0.81[EUR][1000 genomes]
rs162140	0.92[CEU][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs162149	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs162150	0.92[CEU][hapmap];0.92[YRI][hapmap];0.89[EUR][1000 genomes]
rs162473	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs162611	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs170734	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs193072	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2617507	0.83[EUR][1000 genomes]
rs325200	0.81[EUR][1000 genomes]
rs325217	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs326463	0.84[EUR][1000 genomes]
rs326464	0.89[EUR][1000 genomes]
rs326468	0.92[CEU][hapmap];0.80[YRI][hapmap];0.89[EUR][1000 genomes]
rs326469	0.86[EUR][1000 genomes]
rs326485	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs326489	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs327792	0.84[EUR][1000 genomes]
rs327793	0.82[EUR][1000 genomes]
rs327803	0.83[EUR][1000 genomes]
rs327807	0.85[CEU][hapmap]
rs330419	0.82[JPT][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs330421	0.92[CEU][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs330422	0.91[CEU][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs331543	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs331545	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs331549	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs331918	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs331926	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs331929	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs331931	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34489	0.92[CEU][hapmap]
rs34496	0.85[CEU][hapmap]
rs366353	0.88[CEU][hapmap]
rs4565239	0.85[CEU][hapmap]
rs466340	0.84[EUR][1000 genomes]
rs539024	0.82[CEU][hapmap]
rs692832	0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs751878	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7718898	0.80[YRI][hapmap]
rs992773	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs992775	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	nsv882416	chr5:98146106-98312447	Bivalent/Poised TSS Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs331930	RGMB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:98161000-98175400	Weak transcription	Primary T cells from cord blood	blood
2	chr5:98164000-98175200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr5:98169200-98175000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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