Variant report

Variant	rs2545730
Chromosome Location	chr5:98109985-98109986
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	GATA2	chr5:98108248-98110520	SH-SY5Y	brain:	n/a	chr5:98109257-98109267
2	SIN3AK20	chr5:98108522-98110761	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr5:98109884-98110494	H1-hESC	embryonic stem cell:	n/a	n/a
4	FOXA2	chr5:98109862-98110612	A549	lung:	n/a	n/a
5	CREB1	chr5:98108513-98110448	GM12878	blood:	n/a	n/a
6	TCF12	chr5:98108409-98110611	A549	lung:	n/a	chr5:98110256-98110265
7	TCF12	chr5:98108598-98110530	ECC-1	luminal epithelium:	n/a	chr5:98110256-98110265
8	MAX	chr5:98108437-98110865	HepG2	liver:	n/a	chr5:98109181-98109191
9	POLR2A	chr5:98109884-98110110	A549	lung:	n/a	n/a
10	CTCF	chr5:98109980-98110130	HBMEC	blood vessel:	n/a	n/a
11	POLR2A	chr5:98108735-98110399	GM19193	blood:	n/a	n/a
12	POLR2A	chr5:98108625-98110318	GM15510	blood:	n/a	n/a
13	MAZ	chr5:98108020-98110605	IMR90	lung:	n/a	chr5:98109181-98109191
14	BACH1	chr5:98109112-98110115	H1-hESC	embryonic stem cell:	n/a	n/a
15	MAX	chr5:98108320-98110731	HCT-116	colon:	n/a	chr5:98109181-98109191
16	BHLHE40	chr5:98108963-98110192	HepG2	liver:	n/a	chr5:98109564-98109580 chr5:98109569-98109585 chr5:98109590-98109606 chr5:98109572-98109588 chr5:98109985-98110001 chr5:98110094-98110110
17	CTCF	chr5:98109880-98110030	GM12864	blood:	n/a	n/a
18	SMARCC1	chr5:98109332-98110683	Hela-S3	cervix:	n/a	n/a
19	MAX	chr5:98108518-98110763	MCF-7	breast:	n/a	chr5:98109181-98109191
20	BCLAF1	chr5:98109883-98110421	GM12878	blood:	n/a	chr5:98110097-98110110 chr5:98110092-98110105 chr5:98110093-98110106
21	MYC	chr5:98109982-98110625	MCF10A-Er-Src	breast:	n/a	n/a
22	RFX5	chr5:98108655-98110586	Hela-S3	cervix:	n/a	chr5:98108834-98108843
23	CTCF	chr5:98109920-98110070	SK-N-SH_RA	brain:	n/a	n/a
24	POLR2A	chr5:98109967-98110156	H1-hESC	embryonic stem cell:	n/a	n/a
25	MYC	chr5:98108670-98110578	MCF10A-Er-Src	breast:	n/a	chr5:98109181-98109191
26	CTCF	chr5:98109880-98110030	GM12874	blood:	n/a	n/a
27	POLR2A	chr5:98108523-98110482	GM12878	blood:	n/a	n/a
28	POLR2A	chr5:98109964-98110280	Hela-S3	cervix:	n/a	n/a
29	ZNF143	chr5:98108912-98110231	GM12878	blood:	n/a	chr5:98109181-98109191 chr5:98109353-98109363 chr5:98109591-98109601
30	POLR2A	chr5:98108421-98110443	MCF10A-Er-Src	breast:	n/a	n/a
31	MAX	chr5:98108627-98110737	GM12878	blood:	n/a	chr5:98109181-98109191
32	ELF1	chr5:98108548-98110605	GM12878	blood:	n/a	chr5:98109539-98109548 chr5:98109449-98109461 chr5:98109535-98109547
33	SIN3A	chr5:98109879-98110274	GM12878	blood:	n/a	chr5:98109985-98109998 chr5:98110167-98110180
34	HCFC1	chr5:98108112-98110714	Hela-S3	cervix:	n/a	n/a
35	CTCF	chr5:98109860-98110010	GM12875	blood:	n/a	n/a
36	E2F6	chr5:98108284-98110633	A549	lung:	n/a	chr5:98109353-98109363 chr5:98108835-98108844 chr5:98109181-98109190 chr5:98109594-98109604 chr5:98109574-98109584
37	POLR2A	chr5:98108575-98110513	GM12892	blood:	n/a	n/a
38	POLR2A	chr5:98108489-98110447	HUVEC	blood vessel:	n/a	n/a
39	RCOR1	chr5:98108644-98110612	Hela-S3	cervix:	n/a	n/a
40	MYC	chr5:98108396-98110663	A549	lung:	n/a	chr5:98109181-98109191
41	CTCF	chr5:98109940-98110090	NHEK	skin:	n/a	n/a
42	TBP	chr5:98109972-98110461	H1-hESC	embryonic stem cell:	n/a	n/a
43	PAX5	chr5:98109223-98110247	GM12892	blood:	n/a	n/a
44	POLR2A	chr5:98108583-98110401	Hela-S3	cervix:	n/a	n/a
45	POLR2A	chr5:98108595-98110320	HUVEC	blood vessel:	n/a	n/a
46	FOXA1	chr5:98109948-98110517	HepG2	liver:	n/a	n/a
47	POLR2A	chr5:98108439-98110648	H1-hESC	embryonic stem cell:	n/a	n/a
48	POLR2A	chr5:98108566-98110382	MCF-7	breast:	n/a	n/a
49	TAF1	chr5:98109005-98110190	HepG2	liver:	n/a	n/a
50	MXI1	chr5:98108693-98110720	HepG2	liver:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr5:98109981-98110031	HRPEpiC	eye:	n/a
2	chr5:98109981-98110031	T-47D	breast:	n/a
3	chr5:98109981-98110031	HMEC	breast:	n/a
4	chr5:98109981-98110031	HNPCEpiC	eye:	n/a
5	chr5:98109981-98110031	Hepatocyte	liver:	n/a
6	chr5:98109981-98110031	LNCaP	prostate:	n/a
7	chr5:98109981-98110031	SK-N-SH_RA	brain:	n/a
8	chr5:98109981-98110031	BJ	skin:	n/a
9	chr5:98109981-98110031	NH-A	brain:	n/a
10	chr5:98109981-98110031	MCF10A-Er-Src	breast:	n/a
11	chr5:98109981-98110031	MCF-7	breast:	n/a
12	chr5:98109981-98110031	CMK	blood:	n/a
13	chr5:98109981-98110031	HEK293	kidney:	embryo
14	chr5:98109981-98110031	SK-N-SH	brain:	n/a
15	chr5:98109981-98110031	K562	blood:	n/a
16	chr5:98109981-98110031	HCM	heart:	n/a
17	chr5:98109981-98110031	GM06990	blood:	n/a
18	chr5:98109981-98110031	ovcar-3	ovarian:	n/a
19	chr5:98109981-98110031	HL-60	blood:	n/a
20	chr5:98109981-98110031	NHBE	bronchial:	n/a
21	chr5:98109981-98110031	HUVEC	blood vessel:	n/a
22	chr5:98109981-98110031	AoSMC	blood vessel:	n/a
23	chr5:98109981-98110031	AG04449	skin:	fetal
24	chr5:98109981-98110031	AG04450	lung:	fetal
25	chr5:98109981-98110031	NB4	blood:	n/a
26	chr5:98109981-98110031	NT2-D1	testis:	n/a
27	chr5:98109981-98110031	HCT-116	colon:	n/a
28	chr5:98109981-98110031	AG09319	gingival:	n/a
29	chr5:98109981-98110031	SK-N-MC	brain:	n/a
30	chr5:98109981-98110031	Hela-S3	cervix:	n/a
31	chr5:98109981-98110031	AG09309	skin:	n/a
32	chr5:98109981-98110031	NHDF-neo	bronchial:	n/a
33	chr5:98109981-98110031	Jurkat	blood:	n/a
34	chr5:98109981-98110031	AG10803	skin:	n/a
35	chr5:98109981-98110031	GM12892	blood:	n/a
36	chr5:98109981-98110031	SKMC	muscle:	n/a
37	chr5:98109981-98110031	HCPEpiC	choroid plexus:	n/a
38	chr5:98109981-98110031	HEEpiC	esophagus:	n/a
39	chr5:98109981-98110031	PrEC	prostate:	n/a
40	chr5:98109981-98110031	PFSK-1	brain:	n/a
41	chr5:98109981-98110031	U87	brain:	n/a
42	chr5:98109981-98110031	HRE	kidney:	n/a
43	chr5:98109981-98110031	HepG2	liver:	n/a
44	chr5:98109981-98110031	A549	lung:	n/a
45	chr5:98109981-98110031	H1-hESC	embryonic stem cell:	embryo
46	chr5:98109981-98110031	GM12891	blood:	n/a
47	chr5:98109981-98110031	BE2_C	brain:	n/a
48	chr5:98109981-98110031	HRCEpiC	kidney:	n/a
49	chr5:98109981-98110031	HCF	heart:	n/a
50	chr5:98109981-98110031	ProgFib	skin:	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:79935178..79936013-chr5:98109913..98110484,2	Hela-S3	cervix:
2	chr5:98103871..98107404-chr5:98108128..98112327,8	MCF-7	breast:
3	chr5:98102131..98106489-chr5:98107320..98111501,11	MCF-7	breast:
4	chr17:59476329..59477978-chr5:98107765..98110191,2	MCF-7	breast:
5	chr5:96517103..96519459-chr5:98107837..98111064,3	MCF-7	breast:

Variant related genes	Relation type
RGMB-AS1	TF binding region
RGMB-AS1	CpG island
ENSG00000251513	Chromatin interaction
ENSG00000267280	Chromatin interaction
ENSG00000267131	Chromatin interaction
ENSG00000169696	Chromatin interaction
ENSG00000121068	Chromatin interaction
ENSG00000174136	Chromatin interaction
ENSG00000058729	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1508792	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1508793	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1818348	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1828169	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1911904	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1979980	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2249797	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2545671	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2545672	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2545673	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2545675	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2545676	0.80[ASN][1000 genomes]
rs2545690	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2545731	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2545732	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2547965	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2547967	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2547970	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2547972	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2662264	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2662267	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2662268	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2662271	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs331551	0.85[ASN][1000 genomes]
rs992592	0.92[AMR][1000 genomes];0.91[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	esv3339628	chr5:98107452-98111750	Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
3	esv3394593	chr5:98108277-98110825	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2545730	RGMB	cis	multi-tissue	Pritchard
rs2545730	RGMB	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:98103800-98112600	Active TSS	Rectal Smooth Muscle	rectum
2	chr5:98104000-98111400	Active TSS	Psoas Muscle	Psoas
3	chr5:98104000-98113400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr5:98104200-98111600	Active TSS	Right Atrium	heart
5	chr5:98104400-98110800	Active TSS	HSMMtube	muscle
6	chr5:98108200-98111000	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr5:98108200-98111000	Active TSS	HUES64 Cell Line	embryonic stem cell
8	chr5:98108200-98111000	Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr5:98108200-98112200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr5:98108200-98112400	Active TSS	Colonic Mucosa	Colon
11	chr5:98108400-98110600	Active TSS	HSMM	muscle
12	chr5:98108400-98110800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr5:98108400-98111000	Active TSS	iPS-15b Cell Line	embryonic stem cell
14	chr5:98108400-98111000	Active TSS	Esophagus	oesophagus
15	chr5:98108400-98111200	Active TSS	H1 Cell Line	embryonic stem cell
16	chr5:98108400-98111200	Active TSS	H9 Cell Line	embryonic stem cell
17	chr5:98108400-98111200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
18	chr5:98108400-98111200	Active TSS	Breast Myoepithelial Primary Cells	Breast
19	chr5:98108400-98111200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr5:98108400-98111200	Active TSS	Brain Angular Gyrus	brain
21	chr5:98108400-98111600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr5:98108400-98111600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
23	chr5:98108400-98111600	Active TSS	Duodenum Smooth Muscle	Duodenum
24	chr5:98108400-98111800	Active TSS	Pancreas	Pancrea
25	chr5:98108400-98112200	Active TSS	Ovary	ovary
26	chr5:98108400-98112400	Active TSS	Brain Inferior Temporal Lobe	brain
27	chr5:98108600-98110400	Active TSS	Colon Smooth Muscle	Colon
28	chr5:98108600-98110400	Active TSS	Fetal Brain Female	brain
29	chr5:98108600-98110600	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
30	chr5:98108600-98110800	Active TSS	iPS-20b Cell Line	embryonic stem cell
31	chr5:98108600-98110800	Active TSS	Brain Hippocampus Middle	brain
32	chr5:98108600-98110800	Active TSS	Small Intestine	intestine
33	chr5:98108600-98110800	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
34	chr5:98108600-98111000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr5:98108600-98111000	Active TSS	HUES48 Cell Line	embryonic stem cell
36	chr5:98108600-98111200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr5:98108600-98111200	Active TSS	Brain Anterior Caudate	brain
38	chr5:98108600-98111200	Active TSS	Brain Cingulate Gyrus	brain
39	chr5:98108600-98111200	Active TSS	Fetal Kidney	kidney
40	chr5:98108600-98111200	Active TSS	Left Ventricle	heart
41	chr5:98108600-98111600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr5:98108800-98110200	Active TSS	Primary T cells from cord blood	blood
43	chr5:98108800-98110200	Active TSS	NHDF-Ad	bronchial
44	chr5:98108800-98110400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr5:98108800-98110400	Flanking Active TSS	Primary hematopoietic stem cells	blood
46	chr5:98108800-98110400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr5:98108800-98110400	Active TSS	Liver	Liver
48	chr5:98108800-98110400	Active TSS	Osteobl	bone
49	chr5:98108800-98110600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr5:98108800-98110600	Active TSS	Fetal Intestine Large	intestine

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