Variant report

Variant	rs161945
Chromosome Location	chr5:98180947-98180948
allele	A/G
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	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs152034	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs161734	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161736	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161737	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161738	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161739	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161744	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161745	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161746	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs161749	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs161750	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161940	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs161957	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2545733	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2545734	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2545735	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2545736	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2545737	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2545738	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2545739	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2545740	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2578576	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2578577	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2617514	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs325199	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs325203	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs325204	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs325208	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs325209	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs325214	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs326487	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs331541	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs331542	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs331544	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs331548	0.91[EUR][1000 genomes]
rs331927	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs331928	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs469519	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs992774	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[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
rs161945	RGMB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:98175600-98190000	Weak transcription	HUVEC	blood vessel
2	chr5:98175800-98190600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr5:98179800-98181000	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
4	chr5:98179800-98181200	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
5	chr5:98180200-98181000	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr5:98180200-98213600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr5:98180800-98181000	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr5:98180800-98195200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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