Variant report

Variant	rs2545731
Chromosome Location	chr5:98109416-98109417
allele	A/C
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	TAF1	chr5:98108860-98109713	A549	lung:	n/a	n/a
2	GATA2	chr5:98108248-98110520	SH-SY5Y	brain:	n/a	chr5:98109257-98109267
3	YY1	chr5:98108736-98109520	H1-hESC	embryonic stem cell:	n/a	chr5:98109463-98109477 chr5:98109356-98109367 chr5:98109452-98109463
4	SIN3AK20	chr5:98108522-98110761	SK-N-SH	brain:	n/a	n/a
5	GABPA	chr5:98108477-98109459	MCF-7	breast:	n/a	chr5:98109181-98109190
6	MYBL2	chr5:98108793-98109596	HepG2	liver:	n/a	n/a
7	POLR2A	chr5:98108546-98109603	SK-N-SH	brain:	n/a	n/a
8	MAX	chr5:98108503-98109661	SK-N-SH	brain:	n/a	chr5:98109181-98109191
9	MYC	chr5:98108684-98109852	MCF-7	breast:	n/a	chr5:98109181-98109191
10	POLR2A	chr5:98108841-98109717	GM12892	blood:	n/a	n/a
11	CREB1	chr5:98108513-98110448	GM12878	blood:	n/a	n/a
12	TCF12	chr5:98108409-98110611	A549	lung:	n/a	chr5:98110256-98110265
13	POLR2A	chr5:98108580-98109715	ECC-1	luminal epithelium:	n/a	n/a
14	POU2F2	chr5:98108919-98109431	GM12878	blood:	n/a	n/a
15	TCF12	chr5:98108598-98110530	ECC-1	luminal epithelium:	n/a	chr5:98110256-98110265
16	MAX	chr5:98108437-98110865	HepG2	liver:	n/a	chr5:98109181-98109191
17	CREB1	chr5:98108552-98109792	H1-hESC	embryonic stem cell:	n/a	n/a
18	CREB1	chr5:98108589-98109801	A549	lung:	n/a	n/a
19	POLR2A	chr5:98108914-98109809	A549	lung:	n/a	n/a
20	POLR2A	chr5:98108735-98110399	GM19193	blood:	n/a	n/a
21	YY1	chr5:98108951-98109737	ECC-1	luminal epithelium:	n/a	chr5:98109590-98109604 chr5:98109463-98109477 chr5:98109356-98109367 chr5:98109452-98109463
22	SP1	chr5:98108640-98109632	GM12878	blood:	n/a	chr5:98109521-98109528 chr5:98109315-98109324 chr5:98109516-98109530 chr5:98109313-98109325 chr5:98109313-98109325 chr5:98109308-98109320 chr5:98109308-98109320 chr5:98109246-98109267 chr5:98109310-98109319
23	POLR2A	chr5:98108625-98110318	GM15510	blood:	n/a	n/a
24	MAZ	chr5:98108020-98110605	IMR90	lung:	n/a	chr5:98109181-98109191
25	GATA3	chr5:98108953-98109607	T-47D	breast:	n/a	chr5:98109257-98109267
26	BACH1	chr5:98109112-98110115	H1-hESC	embryonic stem cell:	n/a	n/a
27	MAX	chr5:98108320-98110731	HCT-116	colon:	n/a	chr5:98109181-98109191
28	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
29	TBP	chr5:98108587-98109747	H1-hESC	embryonic stem cell:	n/a	n/a
30	CTCF	chr5:98109340-98109490	GM12875	blood:	n/a	n/a
31	SMARCC1	chr5:98109332-98110683	Hela-S3	cervix:	n/a	n/a
32	POLR2A	chr5:98108473-98109656	PANC-1	pancreas:	n/a	n/a
33	MAX	chr5:98108518-98110763	MCF-7	breast:	n/a	chr5:98109181-98109191
34	POLR2A	chr5:98107933-98109677	SK-N-SH	brain:	n/a	n/a
35	YY1	chr5:98108718-98109513	ECC-1	luminal epithelium:	n/a	chr5:98109463-98109477 chr5:98109356-98109367 chr5:98109452-98109463
36	TBP	chr5:98108991-98109468	HepG2	liver:	n/a	n/a
37	RFX5	chr5:98108655-98110586	Hela-S3	cervix:	n/a	chr5:98108834-98108843
38	FOS	chr5:98109018-98109592	Hela-S3	cervix:	n/a	chr5:98109313-98109322 chr5:98109200-98109211
39	CTCF	chr5:98109400-98109550	GM12870	blood:	n/a	n/a
40	CREB1	chr5:98108614-98109781	H1-hESC	embryonic stem cell:	n/a	n/a
41	MYC	chr5:98108670-98110578	MCF10A-Er-Src	breast:	n/a	chr5:98109181-98109191
42	EGR1	chr5:98108989-98109472	GM12878	blood:	n/a	chr5:98109183-98109197 chr5:98109192-98109216
43	POLR2A	chr5:98108523-98110482	GM12878	blood:	n/a	n/a
44	REST	chr5:98109241-98109524	HepG2	liver:	n/a	n/a
45	TEAD4	chr5:98108976-98109593	H1-hESC	embryonic stem cell:	n/a	n/a
46	STAT1	chr5:98108803-98109501	GM12878	blood:	n/a	chr5:98108922-98108934 chr5:98109183-98109195
47	ZNF143	chr5:98108912-98110231	GM12878	blood:	n/a	chr5:98109181-98109191 chr5:98109353-98109363 chr5:98109591-98109601
48	YY1	chr5:98108999-98109416	HCT-116	colon:	n/a	chr5:98109356-98109367
49	POLR2A	chr5:98108421-98110443	MCF10A-Er-Src	breast:	n/a	n/a
50	POLR2A	chr5:98108898-98109786	GM12892	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr5:98109366-98109416	NB4	blood:	n/a
2	chr5:98109366-98109416	Hepatocyte	liver:	n/a
3	chr5:98109366-98109416	HPAEpiC	pulmonary alveolar:	n/a
4	chr5:98109366-98109416	PFSK-1	brain:	n/a
5	chr5:98109366-98109416	A549	lung:	n/a
6	chr5:98109366-98109416	SK-N-SH	brain:	n/a
7	chr5:98109366-98109416	RPTEC	kidney:	n/a
8	chr5:98109366-98109416	HCM	heart:	n/a
9	chr5:98109366-98109416	HRE	kidney:	n/a
10	chr5:98109366-98109416	NHBE	bronchial:	n/a
11	chr5:98109366-98109416	HIPEpiC	eye:	n/a
12	chr5:98109366-98109416	AG09319	gingival:	n/a
13	chr5:98109366-98109416	GM12891	blood:	n/a
14	chr5:98109366-98109416	HCF	heart:	n/a
15	chr5:98109366-98109416	AG04450	lung:	fetal
16	chr5:98109366-98109416	SAEC	small airway:	n/a
17	chr5:98109366-98109416	ProgFib	skin:	n/a
18	chr5:98109366-98109416	HEEpiC	esophagus:	n/a
19	chr5:98109366-98109416	IMR90	lung:	fetal
20	chr5:98109366-98109416	H1-hESC	embryonic stem cell:	embryo
21	chr5:98109366-98109416	ovcar-3	ovarian:	n/a
22	chr5:98109366-98109416	Jurkat	blood:	n/a
23	chr5:98109366-98109416	NH-A	brain:	n/a
24	chr5:98109366-98109416	MCF-7	breast:	n/a
25	chr5:98109366-98109416	BE2_C	brain:	n/a
26	chr5:98109366-98109416	Hela-S3	cervix:	n/a
27	chr5:98109366-98109416	HEK293	kidney:	embryo
28	chr5:98109366-98109416	U87	brain:	n/a
29	chr5:98109366-98109416	HRPEpiC	eye:	n/a
30	chr5:98109366-98109416	AG10803	skin:	n/a
31	chr5:98109366-98109416	GM12878	blood:	n/a
32	chr5:98109366-98109416	BJ	skin:	n/a
33	chr5:98109366-98109416	NT2-D1	testis:	n/a
34	chr5:98109366-98109416	HUVEC	blood vessel:	n/a
35	chr5:98109366-98109416	HRCEpiC	kidney:	n/a
36	chr5:98109366-98109416	ECC-1	luminal epithelium:	n/a
37	chr5:98109366-98109416	SK-N-MC	brain:	n/a
38	chr5:98109366-98109416	MCF10A-Er-Src	breast:	n/a
39	chr5:98109366-98109416	HCT-116	colon:	n/a
40	chr5:98109366-98109416	HL-60	blood:	n/a
41	chr5:98109366-98109416	PANC-1	pancreas:	n/a
42	chr5:98109366-98109416	HCPEpiC	choroid plexus:	n/a
43	chr5:98109366-98109416	K562	blood:	n/a
44	chr5:98109366-98109416	LNCaP	prostate:	n/a
45	chr5:98109366-98109416	GM06990	blood:	n/a
46	chr5:98109366-98109416	PrEC	prostate:	n/a
47	chr5:98109366-98109416	AoSMC	blood vessel:	n/a
48	chr5:98109366-98109416	AG09309	skin:	n/a
49	chr5:98109366-98109416	HAEpiC	amniotic membrane:	n/a
50	chr5:98109366-98109416	NHDF-neo	bronchial:	n/a

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

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

Extended variants
information (count: 27 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1508792	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1508793	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1818348	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1828169	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1911904	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1979980	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2249797	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2545671	0.83[EUR][1000 genomes]
rs2545672	0.83[EUR][1000 genomes]
rs2545673	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2545675	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2545690	0.83[EUR][1000 genomes]
rs2545730	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2545732	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2547965	0.83[EUR][1000 genomes]
rs2547967	0.83[EUR][1000 genomes]
rs2547970	0.80[EUR][1000 genomes]
rs2547972	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2662264	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2662267	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2662268	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2662271	0.82[EUR][1000 genomes]
rs331551	0.84[ASN][1000 genomes]
rs992592	0.83[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2545731	RGMB-AS1	cis	Muscle Skeletal	GTEx
rs2545731	RGMB	cis	multi-tissue	Pritchard
rs2545731	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	chr5:98104400-98109800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr5:98104400-98110800	Active TSS	HSMMtube	muscle
7	chr5:98107400-98109600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr5:98108200-98111000	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr5:98108200-98111000	Active TSS	HUES64 Cell Line	embryonic stem cell
10	chr5:98108200-98111000	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr5:98108200-98112200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr5:98108200-98112400	Active TSS	Colonic Mucosa	Colon
13	chr5:98108400-98109600	Active TSS	Brain Germinal Matrix	brain
14	chr5:98108400-98110600	Active TSS	HSMM	muscle
15	chr5:98108400-98110800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr5:98108400-98111000	Active TSS	iPS-15b Cell Line	embryonic stem cell
17	chr5:98108400-98111000	Active TSS	Esophagus	oesophagus
18	chr5:98108400-98111200	Active TSS	H1 Cell Line	embryonic stem cell
19	chr5:98108400-98111200	Active TSS	H9 Cell Line	embryonic stem cell
20	chr5:98108400-98111200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
21	chr5:98108400-98111200	Active TSS	Breast Myoepithelial Primary Cells	Breast
22	chr5:98108400-98111200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr5:98108400-98111200	Active TSS	Brain Angular Gyrus	brain
24	chr5:98108400-98111600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr5:98108400-98111600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
26	chr5:98108400-98111600	Active TSS	Duodenum Smooth Muscle	Duodenum
27	chr5:98108400-98111800	Active TSS	Pancreas	Pancrea
28	chr5:98108400-98112200	Active TSS	Ovary	ovary
29	chr5:98108400-98112400	Active TSS	Brain Inferior Temporal Lobe	brain
30	chr5:98108600-98109600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr5:98108600-98110400	Active TSS	Colon Smooth Muscle	Colon
32	chr5:98108600-98110400	Active TSS	Fetal Brain Female	brain
33	chr5:98108600-98110600	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
34	chr5:98108600-98110800	Active TSS	iPS-20b Cell Line	embryonic stem cell
35	chr5:98108600-98110800	Active TSS	Brain Hippocampus Middle	brain
36	chr5:98108600-98110800	Active TSS	Small Intestine	intestine
37	chr5:98108600-98110800	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
38	chr5:98108600-98111000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr5:98108600-98111000	Active TSS	HUES48 Cell Line	embryonic stem cell
40	chr5:98108600-98111200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr5:98108600-98111200	Active TSS	Brain Anterior Caudate	brain
42	chr5:98108600-98111200	Active TSS	Brain Cingulate Gyrus	brain
43	chr5:98108600-98111200	Active TSS	Fetal Kidney	kidney
44	chr5:98108600-98111200	Active TSS	Left Ventricle	heart
45	chr5:98108600-98111600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr5:98108800-98109600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr5:98108800-98109800	Active TSS	Muscle Satellite Cultured Cells	--
48	chr5:98108800-98109800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr5:98108800-98109800	Active TSS	Fetal Intestine Small	intestine
50	chr5:98108800-98110200	Active TSS	Primary T cells from cord blood	blood

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