Variant report

Variant	rs1002859
Chromosome Location	chr5:98111947-98111948
allele	A/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	FOS	chr5:98111792-98112322	MCF10A-Er-Src	breast:	n/a	n/a
2	MYC	chr5:98111568-98112323	MCF10A-Er-Src	breast:	n/a	n/a
3	STAT3	chr5:98111573-98112318	MCF10A-Er-Src	breast:	n/a	n/a
4	MAFK	chr5:98111647-98112475	IMR90	lung:	n/a	chr5:98112337-98112352 chr5:98112338-98112349 chr5:98111723-98111733 chr5:98112337-98112348 chr5:98112338-98112349 chr5:98112336-98112350 chr5:98112337-98112348 chr5:98112337-98112353
5	POLR2A	chr5:98103782-98112496	IMR90	lung:	n/a	n/a
6	POLR2A	chr5:98111924-98111962	ProgFib	skin:	n/a	n/a
7	CEBPB	chr5:98111713-98112332	IMR90	lung:	n/a	n/a
8	MXI1	chr5:98107889-98112517	IMR90	lung:	n/a	n/a
9	NFIC	chr5:98111828-98112543	SK-N-SH	brain:	n/a	n/a
10	FOS	chr5:98111585-98112363	MCF10A-Er-Src	breast:	n/a	n/a
11	CHD1	chr5:98103004-98112580	IMR90	lung:	n/a	chr5:98110353-98110363 chr5:98104638-98104648
12	POLR2A	chr5:98109979-98112498	SK-N-SH	brain:	n/a	n/a
13	MXI1	chr5:98107942-98112468	SK-N-SH	brain:	n/a	n/a
14	STAT3	chr5:98111757-98112152	MCF10A-Er-Src	breast:	n/a	n/a
15	MYC	chr5:98111065-98112360	MCF10A-Er-Src	breast:	n/a	chr5:98111330-98111339
16	FOS	chr5:98111429-98112339	MCF10A-Er-Src	breast:	n/a	chr5:98111490-98111500
17	FOS	chr5:98111523-98112302	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:98111277..98112925-chr5:98127736..98129977,2	MCF-7	breast:
2	chr5:98103871..98107404-chr5:98108128..98112327,8	MCF-7	breast:

Variant related genes	Relation type
RGMB-AS1	TF binding region
RGMB	TF binding region
ENSG00000174136	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1002952	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13541	0.81[CHD][hapmap]
rs1508792	0.95[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs1508793	0.95[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs1818348	0.82[ASN][1000 genomes]
rs1828169	0.95[CHB][hapmap];0.86[CHD][hapmap];0.82[ASN][1000 genomes]
rs1911904	0.84[CHB][hapmap]
rs1979980	0.95[CHB][hapmap];0.84[CHD][hapmap];0.82[ASN][1000 genomes]
rs2249797	0.82[ASN][1000 genomes]
rs2250807	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2545673	0.84[CHB][hapmap]
rs2545676	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2545732	0.83[ASN][1000 genomes]
rs2547973	0.86[ASN][1000 genomes]
rs2662258	0.81[CHB][hapmap];0.86[CHD][hapmap]
rs2662264	0.84[CHB][hapmap]
rs331550	1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs331551	0.95[CHB][hapmap];0.91[CHD][hapmap];0.84[ASN][1000 genomes]
rs331552	1.00[CHB][hapmap];0.93[JPT][hapmap];0.97[ASN][1000 genomes]
rs970079	0.90[CHB][hapmap]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1002859	RGMB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:108 , 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	chr5:98104000-98113400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr5:98108200-98112200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr5:98108200-98112400	Active TSS	Colonic Mucosa	Colon
5	chr5:98108400-98112200	Active TSS	Ovary	ovary
6	chr5:98108400-98112400	Active TSS	Brain Inferior Temporal Lobe	brain
7	chr5:98108800-98113000	Active TSS	NH-A	brain
8	chr5:98108800-98113000	Active TSS	NHEK	skin
9	chr5:98108800-98113800	Active TSS	Stomach Smooth Muscle	stomach
10	chr5:98109200-98113200	Active TSS	Rectal Mucosa Donor 29	rectum
11	chr5:98109400-98112400	Transcr. at gene 5' and 3'	NHLF	lung
12	chr5:98109400-98113400	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr5:98109400-98113800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr5:98109600-98119200	Transcr. at gene 5' and 3'	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr5:98109800-98112400	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr5:98109800-98114600	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
17	chr5:98110200-98125200	Transcr. at gene 5' and 3'	NHDF-Ad	bronchial
18	chr5:98110400-98112400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr5:98110400-98112600	Flanking Active TSS	Fetal Brain Female	brain
20	chr5:98110400-98113400	Transcr. at gene 5' and 3'	Osteobl	bone
21	chr5:98110400-98119200	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr5:98110600-98112000	Transcr. at gene 5' and 3'	HSMM	muscle
23	chr5:98110600-98112200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
24	chr5:98110600-98112400	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr5:98110600-98113600	Active TSS	Fetal Intestine Small	intestine
26	chr5:98110600-98115200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr5:98110800-98112000	Enhancers	Primary B cells from peripheral blood	blood
28	chr5:98110800-98112000	Flanking Active TSS	Fetal Brain Male	brain
29	chr5:98110800-98112400	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr5:98110800-98112400	Flanking Active TSS	HUVEC	blood vessel
31	chr5:98110800-98113400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr5:98110800-98113400	Enhancers	Primary T helper cells fromperipheralblood	blood
33	chr5:98110800-98115200	Weak transcription	Lung	lung
34	chr5:98110800-98118600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr5:98110800-98123200	Weak transcription	Aorta	Aorta
36	chr5:98111000-98112000	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
37	chr5:98111000-98112000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr5:98111000-98112000	Enhancers	Brain Substantia Nigra	brain
39	chr5:98111000-98112200	Enhancers	Primary T helper naive cells from peripheral blood	blood
40	chr5:98111000-98112400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
41	chr5:98111000-98112400	Enhancers	Right Ventricle	heart
42	chr5:98111000-98112400	Flanking Active TSS	Hela-S3	cervix
43	chr5:98111000-98115200	Weak transcription	Esophagus	oesophagus
44	chr5:98111000-98116200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr5:98111000-98118600	Weak transcription	Gastric	stomach
46	chr5:98111000-98128800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr5:98111000-98131800	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr5:98111200-98112000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
49	chr5:98111200-98112200	Flanking Active TSS	HMEC	breast
50	chr5:98111200-98112400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle

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