Variant report

Variant	rs2545675
Chromosome Location	chr5:98105191-98105192
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	MAX	chr5:98105071-98105764	ECC-1	luminal epithelium:	n/a	n/a
2	FOXP2	chr5:98105107-98105446	PFSK-1	brain:	n/a	n/a
3	CTCF	chr5:98103774-98105621	GM12878	blood:	n/a	chr5:98104934-98104947 chr5:98104931-98104949 chr5:98104933-98104954
4	ZNF143	chr5:98104707-98105688	H1-hESC	embryonic stem cell:	n/a	n/a
5	MAX	chr5:98105016-98105848	ECC-1	luminal epithelium:	n/a	n/a
6	TCF12	chr5:98103702-98106617	SK-N-SH	brain:	n/a	n/a
7	CEBPB	chr5:98103920-98105849	IMR90	lung:	n/a	n/a
8	POLR2A	chr5:98104495-98105818	H1-neurons	neurons:	n/a	n/a
9	SIN3A	chr5:98103375-98106650	H1-hESC	embryonic stem cell:	n/a	chr5:98103604-98103613
10	TBP	chr5:98104562-98106316	H1-hESC	embryonic stem cell:	n/a	n/a
11	TCF7L2	chr5:98104758-98106785	HCT-116	colon:	n/a	n/a
12	RCOR1	chr5:98103712-98107759	IMR90	lung:	n/a	n/a
13	MXI1	chr5:98104796-98105317	H1-hESC	embryonic stem cell:	n/a	n/a
14	SIN3AK20	chr5:98104719-98106946	SK-N-SH	brain:	n/a	n/a
15	ELF1	chr5:98104534-98105468	GM12878	blood:	n/a	chr5:98104747-98104756 chr5:98104670-98104679
16	YY1	chr5:98104803-98105412	SK-N-SH	brain:	n/a	n/a
17	SMC3	chr5:98103216-98107662	SK-N-SH	brain:	n/a	chr5:98104937-98104947 chr5:98104933-98104947
18	MAZ	chr5:98103628-98107877	IMR90	lung:	n/a	chr5:98104887-98104896 chr5:98104605-98104615
19	CHD2	chr5:98104476-98105368	H1-hESC	embryonic stem cell:	n/a	chr5:98104638-98104648
20	CTBP2	chr5:98103882-98106770	H1-hESC	embryonic stem cell:	n/a	n/a
21	TAF1	chr5:98104550-98105689	H1-neurons	neurons:	n/a	n/a
22	MAX	chr5:98105126-98105334	HepG2	liver:	n/a	n/a
23	ZNF263	chr5:98103812-98107566	HEK293-T-REx	kidney:	n/a	chr5:98104029-98104038
24	TCF12	chr5:98104738-98105621	SK-N-SH	brain:	n/a	n/a
25	MAX	chr5:98104732-98105775	SK-N-SH	brain:	n/a	chr5:98104887-98104896
26	FOXA2	chr5:98104998-98105699	A549	lung:	n/a	n/a
27	POLR2A	chr5:98103782-98112496	IMR90	lung:	n/a	n/a
28	POLR2A	chr5:98104331-98107644	U87	brain:	n/a	n/a
29	TAF1	chr5:98104682-98105293	H1-neurons	neurons:	n/a	n/a
30	POLR2A	chr5:98104882-98105639	SK-N-SH	brain:	n/a	n/a
31	POLR2A	chr5:98104325-98107650	U87	brain:	n/a	n/a
32	FOXA2	chr5:98105111-98105491	A549	lung:	n/a	n/a
33	POLR2A	chr5:98104689-98105243	H1-hESC	embryonic stem cell:	n/a	n/a
34	MYC	chr5:98105088-98105359	H1-hESC	embryonic stem cell:	n/a	n/a
35	RAD21	chr5:98103207-98107631	IMR90	lung:	n/a	chr5:98104757-98104769 chr5:98104608-98104620 chr5:98104932-98104951 chr5:98104937-98104949 chr5:98104937-98104947
36	PBX3	chr5:98104784-98105585	SK-N-SH	brain:	n/a	n/a
37	RAD21	chr5:98103065-98107819	SK-N-SH	brain:	n/a	chr5:98104757-98104769 chr5:98104608-98104620 chr5:98104932-98104951 chr5:98104937-98104949 chr5:98104937-98104947
38	MAX	chr5:98103833-98105641	SK-N-SH	brain:	n/a	chr5:98104887-98104896 chr5:98104605-98104615
39	CTCF	chr5:98103564-98106247	A549	lung:	n/a	chr5:98104934-98104947 chr5:98104931-98104949 chr5:98104933-98104954
40	MAX	chr5:98104974-98105580	A549	lung:	n/a	n/a
41	CTCF	chr5:98103612-98105632	IMR90	lung:	n/a	chr5:98104934-98104947 chr5:98104931-98104949 chr5:98104933-98104954
42	SIN3AK20	chr5:98105167-98105378	PFSK-1	brain:	n/a	n/a
43	CTCF	chr5:98104809-98105196	K562	blood:	n/a	chr5:98104934-98104947 chr5:98104931-98104949 chr5:98104933-98104954
44	POLR2A	chr5:98103751-98106031	H1-hESC	embryonic stem cell:	n/a	n/a
45	ZBTB7A	chr5:98103788-98105827	ECC-1	luminal epithelium:	n/a	n/a
46	FOXA1	chr5:98105066-98105564	HepG2	liver:	n/a	n/a
47	MAX	chr5:98104222-98105836	H1-hESC	embryonic stem cell:	n/a	chr5:98104887-98104896 chr5:98104605-98104615
48	CHD1	chr5:98103004-98112580	IMR90	lung:	n/a	chr5:98110353-98110363 chr5:98104638-98104648
49	CTCF	chr5:98104460-98105510	HCT-116	colon:	n/a	chr5:98104934-98104947 chr5:98104931-98104949 chr5:98104933-98104954
50	TAF1	chr5:98104517-98105865	SK-N-SH	brain:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr5:98105150-98105200	PrEC	prostate:	n/a
2	chr5:98105150-98105200	SK-N-SH	brain:	n/a
3	chr5:98105150-98105200	HRCEpiC	kidney:	n/a
4	chr5:98105150-98105200	PANC-1	pancreas:	n/a
5	chr5:98105150-98105200	MCF-7	breast:	n/a
6	chr5:98105150-98105200	HCPEpiC	choroid plexus:	n/a
7	chr5:98105150-98105200	AoSMC	blood vessel:	n/a
8	chr5:98105150-98105200	ovcar-3	ovarian:	n/a
9	chr5:98105150-98105200	HRE	kidney:	n/a
10	chr5:98105150-98105200	SK-N-SH_RA	brain:	n/a
11	chr5:98105150-98105200	CMK	blood:	n/a
12	chr5:98105150-98105200	HCM	heart:	n/a
13	chr5:98105150-98105200	NT2-D1	testis:	n/a
14	chr5:98105150-98105200	HEK293	kidney:	embryo
15	chr5:98105150-98105200	Jurkat	blood:	n/a
16	chr5:98105150-98105200	HCT-116	colon:	n/a
17	chr5:98105150-98105200	AG04450	lung:	fetal
18	chr5:98105150-98105200	NHBE	bronchial:	n/a
19	chr5:98105150-98105200	HCF	heart:	n/a
20	chr5:98105150-98105200	K562	blood:	n/a
21	chr5:98105150-98105200	GM12878	blood:	n/a
22	chr5:98105150-98105200	AG09319	gingival:	n/a
23	chr5:98105150-98105200	PFSK-1	brain:	n/a
24	chr5:98105150-98105200	Hepatocyte	liver:	n/a
25	chr5:98105150-98105200	SAEC	small airway:	n/a
26	chr5:98105150-98105200	MCF10A-Er-Src	breast:	n/a
27	chr5:98105150-98105200	HAEpiC	amniotic membrane:	n/a
28	chr5:98105150-98105200	AG10803	skin:	n/a
29	chr5:98105150-98105200	AG09309	skin:	n/a
30	chr5:98105150-98105200	H1-hESC	embryonic stem cell:	embryo
31	chr5:98105150-98105200	GM19239	blood:	n/a
32	chr5:98105150-98105200	HEEpiC	esophagus:	n/a
33	chr5:98105150-98105200	HL-60	blood:	n/a
34	chr5:98105150-98105200	GM12891	blood:	n/a
35	chr5:98105150-98105200	BE2_C	brain:	n/a
36	chr5:98105150-98105200	LNCaP	prostate:	n/a
37	chr5:98105150-98105200	U87	brain:	n/a
38	chr5:98105150-98105200	T-47D	breast:	n/a
39	chr5:98105150-98105200	GM12892	blood:	n/a
40	chr5:98105150-98105200	HepG2	liver:	n/a
41	chr5:98105150-98105200	SKMC	muscle:	n/a
42	chr5:98105150-98105200	HMEC	breast:	n/a
43	chr5:98105150-98105200	AG04449	skin:	fetal
44	chr5:98105150-98105200	HIPEpiC	eye:	n/a
45	chr5:98105150-98105200	SK-N-MC	brain:	n/a
46	chr5:98105150-98105200	HPAEpiC	pulmonary alveolar:	n/a
47	chr5:98105150-98105200	ECC-1	luminal epithelium:	n/a
48	chr5:98105150-98105200	Caco-2	colon:	n/a
49	chr5:98105150-98105200	NH-A	brain:	n/a
50	chr5:98105150-98105200	RPTEC	kidney:	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:98103871..98107404-chr5:98108128..98112327,8	MCF-7	breast:
2	chr13:30995836..30997058-chr5:98104720..98105240,4	HCT-116	colon:
3	chr5:98102131..98106489-chr5:98107320..98111501,11	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CTD-2215E18.1.1-7	chr5:98105140-98105329	NONHSAT102948

Variant related genes	Relation type
RGMB	TF binding region
RGMB	CpG island
ENSG00000174136	Chromatin interaction
ENSG00000225039	Chromatin interaction
ENSG00000246763	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1508792	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1508793	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1818348	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1828169	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1911904	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1979980	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2249797	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2545671	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2545672	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2545673	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2545690	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2545730	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2545731	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2545732	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2547965	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2547967	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2547970	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2547972	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2662264	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2662267	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2662268	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2662271	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs331551	0.83[ASN][1000 genomes]
rs992592	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2545675	RGMB	Cis_1M	lymphoblastoid	RTeQTL
rs2545675	RGMB	cis	multi-tissue	Pritchard
rs2545675	RGMB-AS1	cis	Muscle Skeletal	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:98103200-98107200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr5:98103400-98107400	Active TSS	Aorta	Aorta
3	chr5:98103400-98107600	Active TSS	Brain Anterior Caudate	brain
4	chr5:98103600-98105200	Active TSS	Brain Germinal Matrix	brain
5	chr5:98103800-98105600	Active TSS	iPS-15b Cell Line	embryonic stem cell
6	chr5:98103800-98106200	Active TSS	Fetal Brain Female	brain
7	chr5:98103800-98107400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr5:98103800-98107400	Active TSS	Breast Myoepithelial Primary Cells	Breast
9	chr5:98103800-98107400	Flanking Active TSS	Liver	Liver
10	chr5:98103800-98107400	Active TSS	Brain Angular Gyrus	brain
11	chr5:98103800-98107400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
12	chr5:98103800-98107400	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr5:98103800-98107600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
14	chr5:98103800-98107800	Active TSS	Brain Cingulate Gyrus	brain
15	chr5:98103800-98108000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr5:98103800-98108000	Active TSS	Brain Inferior Temporal Lobe	brain
17	chr5:98103800-98108200	Active TSS	Fetal Kidney	kidney
18	chr5:98103800-98112600	Active TSS	Rectal Smooth Muscle	rectum
19	chr5:98104000-98105200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
20	chr5:98104000-98105200	Active TSS	Fetal Brain Male	brain
21	chr5:98104000-98105400	Active TSS	Esophagus	oesophagus
22	chr5:98104000-98105600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr5:98104000-98106400	Active TSS	NHDF-Ad	bronchial
24	chr5:98104000-98106600	Active TSS	H9 Cell Line	embryonic stem cell
25	chr5:98104000-98106600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr5:98104000-98106600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
27	chr5:98104000-98107000	Active TSS	Stomach Mucosa	stomach
28	chr5:98104000-98107200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr5:98104000-98107200	Active TSS	Gastric	stomach
30	chr5:98104000-98107400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
31	chr5:98104000-98107400	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
32	chr5:98104000-98107400	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
33	chr5:98104000-98107400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr5:98104000-98107400	Active TSS	Brain Substantia Nigra	brain
35	chr5:98104000-98107400	Active TSS	Left Ventricle	heart
36	chr5:98104000-98107400	Active TSS	Ovary	ovary
37	chr5:98104000-98107400	Active TSS	Pancreas	Pancrea
38	chr5:98104000-98107600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
39	chr5:98104000-98107600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr5:98104000-98107600	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
41	chr5:98104000-98107600	Flanking Active TSS	Adipose Nuclei	Adipose
42	chr5:98104000-98107600	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
43	chr5:98104000-98107800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr5:98104000-98108200	Active TSS	Fetal Intestine Large	intestine
45	chr5:98104000-98111400	Active TSS	Psoas Muscle	Psoas
46	chr5:98104000-98113400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr5:98104200-98105200	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood
48	chr5:98104200-98105400	Active TSS	Rectal Mucosa Donor 31	rectum
49	chr5:98104200-98105600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr5:98104200-98105800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell

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