Variant report

Variant	rs2249797
Chromosome Location	chr5:98107341-98107342
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	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	ARID3A	chr5:98107213-98107639	HepG2	liver:	n/a	n/a
5	MAZ	chr5:98107048-98107571	Hela-S3	cervix:	n/a	n/a
6	CTCF	chr5:98107222-98107550	Kidney_OC	kidney:	n/a	n/a
7	CTCF	chr5:98107260-98107410	WI-38	lung:	n/a	n/a
8	STAT3	chr5:98107088-98107666	Hela-S3	cervix:	n/a	n/a
9	SMC3	chr5:98107255-98107646	K562	blood:	n/a	n/a
10	FOXA1	chr5:98107294-98107512	T-47D	breast:	n/a	n/a
11	CTCF	chr5:98107320-98107470	GM12865	blood:	n/a	n/a
12	FOS	chr5:98107241-98107576	MCF10A-Er-Src	breast:	n/a	n/a
13	ATF3	chr5:98107292-98107527	K562	blood:	n/a	n/a
14	HDAC2	chr5:98107302-98107558	H1-hESC	embryonic stem cell:	n/a	n/a
15	CTCF	chr5:98107340-98107490	AG09309	skin:	n/a	n/a
16	CTCF	chr5:98107340-98107490	GM12866	blood:	n/a	n/a
17	ZNF143	chr5:98107234-98107633	GM12878	blood:	n/a	n/a
18	CEBPB	chr5:98106089-98107566	IMR90	lung:	n/a	chr5:98106944-98106961
19	CTCF	chr5:98106527-98107683	IMR90	lung:	n/a	n/a
20	CTCF	chr5:98107305-98107566	LNCaP	prostate:	n/a	n/a
21	CTCF	chr5:98107312-98107575	Spleen_OC	spleen:	n/a	n/a
22	RCOR1	chr5:98106022-98107574	Hela-S3	cervix:	n/a	n/a
23	RAD21	chr5:98107062-98107616	Hela-S3	cervix:	n/a	n/a
24	MAX	chr5:98107044-98107633	SK-N-SH	brain:	n/a	n/a
25	CTCF	chr5:98107319-98107545	HepG2	liver:	n/a	n/a
26	CTCF	chr5:98107234-98107565	Pancreas_OC	pancreas:	n/a	n/a
27	CTCF	chr5:98106954-98107718	HCT-116	colon:	n/a	n/a
28	SIN3AK20	chr5:98107011-98107608	SK-N-SH	brain:	n/a	n/a
29	RAD21	chr5:98107155-98107618	H1-hESC	embryonic stem cell:	n/a	n/a
30	SP1	chr5:98107192-98107664	H1-hESC	embryonic stem cell:	n/a	chr5:98107488-98107500 chr5:98107489-98107498
31	MAZ	chr5:98107264-98107613	K562	blood:	n/a	n/a
32	RAD21	chr5:98107161-98107732	MCF-7	breast:	n/a	n/a
33	CTCF	chr5:98107340-98107490	HAc	cerebellar:	n/a	n/a
34	ATF1	chr5:98107273-98107572	K562	blood:	n/a	n/a
35	CTCF	chr5:98107320-98107470	GM12874	blood:	n/a	n/a
36	TCF12	chr5:98106777-98107721	A549	lung:	n/a	n/a
37	RCOR1	chr5:98103712-98107759	IMR90	lung:	n/a	n/a
38	BHLHE40	chr5:98107253-98107669	GM12878	blood:	n/a	n/a
39	STAT3	chr5:98107238-98107499	MCF10A-Er-Src	breast:	n/a	n/a
40	CTCF	chr5:98107236-98107646	K562	blood:	n/a	n/a
41	CTCF	chr5:98107340-98107490	GM12869	blood:	n/a	n/a
42	FOXM1	chr5:98107156-98107640	GM12878	blood:	n/a	n/a
43	BCLAF1	chr5:98107015-98107639	GM12878	blood:	n/a	n/a
44	ELK1	chr5:98107256-98107583	GM12878	blood:	n/a	n/a
45	CTCF	chr5:98107340-98107490	HBMEC	blood vessel:	n/a	n/a
46	HDAC2	chr5:98107244-98107662	HepG2	liver:	n/a	n/a
47	ELF1	chr5:98107221-98107550	A549	lung:	n/a	n/a
48	CTCF	chr5:98107307-98107560	GM10248	blood:	n/a	n/a
49	SMC3	chr5:98103216-98107662	SK-N-SH	brain:	n/a	chr5:98104937-98104947 chr5:98104933-98104947
50	MAZ	chr5:98103628-98107877	IMR90	lung:	n/a	chr5:98104887-98104896 chr5:98104605-98104615

No.	Distal block	Cell Line	Cell type
1	chr5:98102131..98106489-chr5:98107320..98111501,11	MCF-7	breast:
2	chr5:98103871..98107404-chr5:98108128..98112327,8	MCF-7	breast:
3	chr5:98102950..98105852-chr5:98106707..98108223,2	K562	blood:

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

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1002859	0.82[ASN][1000 genomes]
rs1002952	0.82[ASN][1000 genomes]
rs1508792	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1508793	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1818348	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1828169	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1911904	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1979980	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2250807	0.82[ASN][1000 genomes]
rs2545671	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2545672	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2545673	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2545675	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2545676	0.83[ASN][1000 genomes]
rs2545690	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2545730	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2545731	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2545732	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2547965	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2547967	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2547970	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2547972	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2662264	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2662267	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2662268	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2662271	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs331550	0.82[ASN][1000 genomes]
rs331551	0.86[ASN][1000 genomes]
rs331552	0.82[ASN][1000 genomes]
rs992592	0.92[AMR][1000 genomes];0.95[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2249797	RGMB	cis	multi-tissue	Pritchard
rs2249797	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	chr5:98103400-98107400	Active TSS	Aorta	Aorta
2	chr5:98103400-98107600	Active TSS	Brain Anterior Caudate	brain
3	chr5:98103800-98107400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr5:98103800-98107400	Active TSS	Breast Myoepithelial Primary Cells	Breast
5	chr5:98103800-98107400	Flanking Active TSS	Liver	Liver
6	chr5:98103800-98107400	Active TSS	Brain Angular Gyrus	brain
7	chr5:98103800-98107400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
8	chr5:98103800-98107400	Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr5:98103800-98107600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
10	chr5:98103800-98107800	Active TSS	Brain Cingulate Gyrus	brain
11	chr5:98103800-98108000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr5:98103800-98108000	Active TSS	Brain Inferior Temporal Lobe	brain
13	chr5:98103800-98108200	Active TSS	Fetal Kidney	kidney
14	chr5:98103800-98112600	Active TSS	Rectal Smooth Muscle	rectum
15	chr5:98104000-98107400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
16	chr5:98104000-98107400	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
17	chr5:98104000-98107400	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
18	chr5:98104000-98107400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr5:98104000-98107400	Active TSS	Brain Substantia Nigra	brain
20	chr5:98104000-98107400	Active TSS	Left Ventricle	heart
21	chr5:98104000-98107400	Active TSS	Ovary	ovary
22	chr5:98104000-98107400	Active TSS	Pancreas	Pancrea
23	chr5:98104000-98107600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
24	chr5:98104000-98107600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr5:98104000-98107600	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
26	chr5:98104000-98107600	Flanking Active TSS	Adipose Nuclei	Adipose
27	chr5:98104000-98107600	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
28	chr5:98104000-98107800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr5:98104000-98108200	Active TSS	Fetal Intestine Large	intestine
30	chr5:98104000-98111400	Active TSS	Psoas Muscle	Psoas
31	chr5:98104000-98113400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr5:98104200-98107400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr5:98104200-98108000	Active TSS	Brain Hippocampus Middle	brain
34	chr5:98104200-98111600	Active TSS	Right Atrium	heart
35	chr5:98104400-98107400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr5:98104400-98107400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
37	chr5:98104400-98107400	Active TSS	Osteobl	bone
38	chr5:98104400-98107600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr5:98104400-98107800	Active TSS	NHLF	lung
40	chr5:98104400-98108000	Active TSS	Muscle Satellite Cultured Cells	--
41	chr5:98104400-98108200	Active TSS	Fetal Intestine Small	intestine
42	chr5:98104400-98109800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr5:98104400-98110800	Active TSS	HSMMtube	muscle
44	chr5:98104600-98107400	Flanking Active TSS	Primary hematopoietic stem cells	blood
45	chr5:98104600-98107400	Bivalent/Poised TSS	HepG2	liver
46	chr5:98104600-98107600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
47	chr5:98104600-98107600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr5:98104600-98107600	Active TSS	NH-A	brain
49	chr5:98104600-98107800	Active TSS	HSMM	muscle
50	chr5:98104600-98107800	Active TSS	NHEK	skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links