Variant report

Variant	rs2662264
Chromosome Location	chr5:98099960-98099961
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FAM48A	chr5:98099958-98100070	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:98097815..98101035-chr5:98108800..98111033,3	MCF-7	breast:
2	chr5:98099685..98101972-chr5:98104420..98105934,2	MCF-7	breast:

Variant related genes	Relation type
RGMB	TF binding region
ENSG00000174136	Chromatin interaction
ENSG00000246763	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1002859	0.84[CHB][hapmap]
rs1508792	0.83[CEU][hapmap];0.90[CHB][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1508793	0.82[CEU][hapmap];0.90[CHB][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1818348	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1828169	0.96[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1911904	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1979980	0.82[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2249797	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2250807	0.84[CHB][hapmap]
rs2545671	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2545672	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2545673	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2545675	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2545676	0.84[CHB][hapmap]
rs2545690	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2545730	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2545731	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2545732	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2547965	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2547967	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2547970	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2547972	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2662267	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2662268	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2662271	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs331550	0.85[CHB][hapmap]
rs331551	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs331552	0.85[CHB][hapmap]
rs992592	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2662264	RGMB	cis	multi-tissue	Pritchard
rs2662264	RGMB-AS1	cis	Muscle Skeletal	GTEx
rs2662264	RGMB	cis	uninvolved skin	skin_eQTL
rs2662264	RGMB	Cis_1M	lymphoblastoid	RTeQTL
rs2662264	RGMB	cis	normal skin	skin_eQTL

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:98089600-98104000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr5:98097400-98103200	Weak transcription	HSMMtube	muscle
3	chr5:98098200-98101000	Enhancers	NHDF-Ad	bronchial
4	chr5:98098400-98100400	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr5:98098400-98100600	Enhancers	iPS-20b Cell Line	embryonic stem cell
6	chr5:98098400-98100600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr5:98098400-98100600	Enhancers	Muscle Satellite Cultured Cells	--
8	chr5:98098800-98100000	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr5:98098800-98100000	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr5:98098800-98100600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr5:98098800-98100600	Enhancers	NHLF	lung
12	chr5:98099000-98100000	Enhancers	Osteobl	bone
13	chr5:98099000-98100600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr5:98099200-98100600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr5:98099400-98100000	Enhancers	iPS-15b Cell Line	embryonic stem cell
16	chr5:98099400-98100200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr5:98099400-98102800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr5:98099400-98102800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr5:98099400-98103200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr5:98099400-98103400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr5:98099400-98103400	Weak transcription	Fetal Muscle Leg	muscle
22	chr5:98099400-98104000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr5:98099600-98100600	Enhancers	iPS-18 Cell Line	embryonic stem cell
24	chr5:98099600-98103000	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr5:98099600-98103400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr5:98099600-98103400	Weak transcription	NH-A	brain
27	chr5:98099800-98103000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr5:98099800-98103200	Weak transcription	HSMM	muscle

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