Variant report

Variant	rs2545740
Chromosome Location	chr5:98173242-98173243
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs150935	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs152034	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs161734	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161736	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161737	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161738	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161739	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161744	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161745	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161746	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs161749	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs161750	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161940	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs161945	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161957	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2545733	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2545734	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2545735	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2545736	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2545737	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2545738	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2545739	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2578576	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2578577	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2617514	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs325199	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs325203	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs325204	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs325208	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs325209	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs325214	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs326487	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs331541	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs331542	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs331544	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs331548	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs331927	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs331928	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs469519	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs992774	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[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
rs2545740	RGMB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:7 , 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
4	chr5:98170400-98176600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr5:98172000-98175000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr5:98172200-98179800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr5:98173000-98175200	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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