Variant report

Variant	rs1979980
Chromosome Location	chr5:98107067-98107068
allele	G/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	TCF7L2	chr5:98106777-98107365	PANC-1	pancreas:	n/a	n/a
2	JUND	chr5:98106929-98107552	K562	blood:	n/a	n/a
3	PRDM1	chr5:98106320-98107564	Hela-S3	cervix:	n/a	chr5:98106448-98106463 chr5:98106485-98106500
4	MAZ	chr5:98107048-98107571	Hela-S3	cervix:	n/a	n/a
5	CEBPB	chr5:98106089-98107566	IMR90	lung:	n/a	chr5:98106944-98106961
6	CTCF	chr5:98106527-98107683	IMR90	lung:	n/a	n/a
7	RCOR1	chr5:98106022-98107574	Hela-S3	cervix:	n/a	n/a
8	RAD21	chr5:98107062-98107616	Hela-S3	cervix:	n/a	n/a
9	MAX	chr5:98107044-98107633	SK-N-SH	brain:	n/a	n/a
10	CTCF	chr5:98106954-98107718	HCT-116	colon:	n/a	n/a
11	SIN3AK20	chr5:98107011-98107608	SK-N-SH	brain:	n/a	n/a
12	TCF12	chr5:98106777-98107721	A549	lung:	n/a	n/a
13	RCOR1	chr5:98103712-98107759	IMR90	lung:	n/a	n/a
14	BCLAF1	chr5:98107015-98107639	GM12878	blood:	n/a	n/a
15	SMC3	chr5:98103216-98107662	SK-N-SH	brain:	n/a	chr5:98104937-98104947 chr5:98104933-98104947
16	MAZ	chr5:98103628-98107877	IMR90	lung:	n/a	chr5:98104887-98104896 chr5:98104605-98104615
17	MYC	chr5:98106498-98107685	MCF10A-Er-Src	breast:	n/a	n/a
18	POLR2A	chr5:98105261-98107576	Hela-S3	cervix:	n/a	n/a
19	RFX5	chr5:98106172-98107639	Hela-S3	cervix:	n/a	n/a
20	MYC	chr5:98107003-98107601	MCF10A-Er-Src	breast:	n/a	n/a
21	RAD21	chr5:98107045-98107736	HCT-116	colon:	n/a	n/a
22	IRF3	chr5:98107037-98107096	GM12878	blood:	n/a	n/a
23	SMC3	chr5:98106003-98107608	Hela-S3	cervix:	n/a	n/a
24	ZNF263	chr5:98103812-98107566	HEK293-T-REx	kidney:	n/a	chr5:98104029-98104038
25	GTF2F1	chr5:98106028-98107561	Hela-S3	cervix:	n/a	n/a
26	CTCF	chr5:98106325-98108512	SK-N-SH	brain:	n/a	chr5:98108010-98108017
27	POLR2A	chr5:98103782-98112496	IMR90	lung:	n/a	n/a
28	POLR2A	chr5:98104331-98107644	U87	brain:	n/a	n/a
29	MTA3	chr5:98107013-98107612	GM12878	blood:	n/a	n/a
30	POLR2A	chr5:98104325-98107650	U87	brain:	n/a	n/a
31	RUNX3	chr5:98106960-98107619	GM12878	blood:	n/a	chr5:98107230-98107239 chr5:98107230-98107239
32	RUNX3	chr5:98107000-98107599	GM12878	blood:	n/a	chr5:98107230-98107239 chr5:98107230-98107239
33	WRNIP1	chr5:98107050-98107560	GM12878	blood:	n/a	n/a
34	TCF7L2	chr5:98107028-98107771	HEK293	kidney:	n/a	chr5:98107577-98107586 chr5:98107573-98107589
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	CEBPB	chr5:98105860-98107619	Hela-S3	cervix:	n/a	chr5:98106944-98106961
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	TBL1XR1	chr5:98107017-98107541	GM12878	blood:	n/a	n/a
39	TAF1	chr5:98106965-98107545	SK-N-SH	brain:	n/a	n/a
40	NFE2	chr5:98107029-98107490	GM12878	blood:	n/a	n/a
41	POLR2A	chr5:98107039-98107231	HUVEC	blood vessel:	n/a	n/a
42	POLR2A	chr5:98107016-98107577	H1-neurons	neurons:	n/a	n/a
43	MAFK	chr5:98106765-98107630	Hela-S3	cervix:	n/a	chr5:98107249-98107260
44	GTF3C2	chr5:98106550-98107425	Hela-S3	cervix:	n/a	n/a
45	RAD21	chr5:98107046-98107644	SK-N-SH_RA	brain:	n/a	n/a
46	CHD1	chr5:98103004-98112580	IMR90	lung:	n/a	chr5:98110353-98110363 chr5:98104638-98104648
47	POLR2A	chr5:98106991-98107589	HCT-116	colon:	n/a	n/a
48	BRCA1	chr5:98106483-98107649	Hela-S3	cervix:	n/a	n/a
49	MXI1	chr5:98103700-98107724	IMR90	lung:	n/a	n/a
50	KAP1	chr5:98105735-98107700	HEK293	kidney:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:98103871..98107404-chr5:98108128..98112327,8	MCF-7	breast:
2	chr5:98102950..98105852-chr5:98106707..98108223,2	K562	blood:

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

Extended variants
information (count: 34 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1002859	0.95[CHB][hapmap];0.84[CHD][hapmap];0.82[ASN][1000 genomes]
rs1002952	0.82[ASN][1000 genomes]
rs13541	0.81[CHD][hapmap]
rs1508792	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1508793	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1818348	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1828169	0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1911904	0.85[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2249797	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2250807	0.94[CHB][hapmap];0.82[ASN][1000 genomes]
rs2545671	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2545672	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2545673	0.81[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]
rs2545675	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2545676	0.94[CHB][hapmap];0.83[ASN][1000 genomes]
rs2545690	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2545730	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2545731	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2545732	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2547965	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2547967	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2547970	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2547972	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2662258	0.86[CHD][hapmap]
rs2662264	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]
rs2662267	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2662268	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2662271	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs331550	0.95[CHB][hapmap];0.82[ASN][1000 genomes]
rs331551	0.90[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs331552	0.95[CHB][hapmap];0.82[ASN][1000 genomes]
rs970079	0.85[CHB][hapmap]
rs992592	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[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
rs1979980	RGMB	cis	normal skin	skin_eQTL
rs1979980	RGMB	Cis_1M	lymphoblastoid	RTeQTL
rs1979980	RGMB	cis	multi-tissue	Pritchard

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	chr5:98103800-98107400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr5:98103800-98107400	Active TSS	Breast Myoepithelial Primary Cells	Breast
6	chr5:98103800-98107400	Flanking Active TSS	Liver	Liver
7	chr5:98103800-98107400	Active TSS	Brain Angular Gyrus	brain
8	chr5:98103800-98107400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
9	chr5:98103800-98107400	Active TSS	Pancreatic Islets	Pancreatic Islet
10	chr5:98103800-98107600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
11	chr5:98103800-98107800	Active TSS	Brain Cingulate Gyrus	brain
12	chr5:98103800-98108000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr5:98103800-98108000	Active TSS	Brain Inferior Temporal Lobe	brain
14	chr5:98103800-98108200	Active TSS	Fetal Kidney	kidney
15	chr5:98103800-98112600	Active TSS	Rectal Smooth Muscle	rectum
16	chr5:98104000-98107200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr5:98104000-98107200	Active TSS	Gastric	stomach
18	chr5:98104000-98107400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
19	chr5:98104000-98107400	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
20	chr5:98104000-98107400	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
21	chr5:98104000-98107400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr5:98104000-98107400	Active TSS	Brain Substantia Nigra	brain
23	chr5:98104000-98107400	Active TSS	Left Ventricle	heart
24	chr5:98104000-98107400	Active TSS	Ovary	ovary
25	chr5:98104000-98107400	Active TSS	Pancreas	Pancrea
26	chr5:98104000-98107600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
27	chr5:98104000-98107600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr5:98104000-98107600	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
29	chr5:98104000-98107600	Flanking Active TSS	Adipose Nuclei	Adipose
30	chr5:98104000-98107600	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
31	chr5:98104000-98107800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr5:98104000-98108200	Active TSS	Fetal Intestine Large	intestine
33	chr5:98104000-98111400	Active TSS	Psoas Muscle	Psoas
34	chr5:98104000-98113400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr5:98104200-98107400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr5:98104200-98108000	Active TSS	Brain Hippocampus Middle	brain
37	chr5:98104200-98111600	Active TSS	Right Atrium	heart
38	chr5:98104400-98107400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr5:98104400-98107400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
40	chr5:98104400-98107400	Active TSS	Osteobl	bone
41	chr5:98104400-98107600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr5:98104400-98107800	Active TSS	NHLF	lung
43	chr5:98104400-98108000	Active TSS	Muscle Satellite Cultured Cells	--
44	chr5:98104400-98108200	Active TSS	Fetal Intestine Small	intestine
45	chr5:98104400-98109800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr5:98104400-98110800	Active TSS	HSMMtube	muscle
47	chr5:98104600-98107400	Flanking Active TSS	Primary hematopoietic stem cells	blood
48	chr5:98104600-98107400	Bivalent/Poised TSS	HepG2	liver
49	chr5:98104600-98107600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
50	chr5:98104600-98107600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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