Variant report

Variant	rs2277929
Chromosome Location	chr5:98106025-98106026
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	TCF7L2	chr5:98105601-98106821	Hela-S3	cervix:	n/a	n/a
2	TCF12	chr5:98103702-98106617	SK-N-SH	brain:	n/a	n/a
3	EBF1	chr5:98105741-98106088	GM12878	blood:	n/a	n/a
4	RCOR1	chr5:98106022-98107574	Hela-S3	cervix:	n/a	n/a
5	SIN3A	chr5:98103375-98106650	H1-hESC	embryonic stem cell:	n/a	chr5:98103604-98103613
6	TBP	chr5:98104562-98106316	H1-hESC	embryonic stem cell:	n/a	n/a
7	ELK1	chr5:98105890-98106299	Hela-S3	cervix:	n/a	n/a
8	TCF7L2	chr5:98104758-98106785	HCT-116	colon:	n/a	n/a
9	RCOR1	chr5:98103712-98107759	IMR90	lung:	n/a	n/a
10	SIN3AK20	chr5:98104719-98106946	SK-N-SH	brain:	n/a	n/a
11	SMC3	chr5:98103216-98107662	SK-N-SH	brain:	n/a	chr5:98104937-98104947 chr5:98104933-98104947
12	GTF2F1	chr5:98105987-98106144	H1-hESC	embryonic stem cell:	n/a	n/a
13	MAZ	chr5:98103628-98107877	IMR90	lung:	n/a	chr5:98104887-98104896 chr5:98104605-98104615
14	POLR2A	chr5:98105261-98107576	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr5:98105814-98106600	HUVEC	blood vessel:	n/a	n/a
16	ATF2	chr5:98105994-98106824	GM12878	blood:	n/a	n/a
17	CTBP2	chr5:98103882-98106770	H1-hESC	embryonic stem cell:	n/a	n/a
18	MAX	chr5:98105591-98106774	A549	lung:	n/a	n/a
19	TAF1	chr5:98105961-98106389	H1-hESC	embryonic stem cell:	n/a	n/a
20	NFIC	chr5:98105876-98106850	ECC-1	luminal epithelium:	n/a	n/a
21	MAZ	chr5:98105989-98106132	K562	blood:	n/a	n/a
22	SMC3	chr5:98106003-98107608	Hela-S3	cervix:	n/a	n/a
23	ZNF263	chr5:98103812-98107566	HEK293-T-REx	kidney:	n/a	chr5:98104029-98104038
24	MXI1	chr5:98105919-98106134	H1-hESC	embryonic stem cell:	n/a	n/a
25	HDAC2	chr5:98105971-98106526	HepG2	liver:	n/a	n/a
26	POLR2A	chr5:98103782-98112496	IMR90	lung:	n/a	n/a
27	POLR2A	chr5:98104331-98107644	U87	brain:	n/a	n/a
28	STAT1	chr5:98106002-98106288	GM12878	blood:	n/a	n/a
29	POLR2A	chr5:98104325-98107650	U87	brain:	n/a	n/a
30	TBL1XR1	chr5:98105996-98106618	GM12878	blood:	n/a	n/a
31	RAD21	chr5:98103207-98107631	IMR90	lung:	n/a	chr5:98104757-98104769 chr5:98104608-98104620 chr5:98104932-98104951 chr5:98104937-98104949 chr5:98104937-98104947
32	CHD2	chr5:98105850-98106423	H1-hESC	embryonic stem cell:	n/a	n/a
33	CEBPB	chr5:98105860-98107619	Hela-S3	cervix:	n/a	chr5:98106944-98106961
34	TCF7L2	chr5:98105924-98106528	PANC-1	pancreas:	n/a	n/a
35	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
36	CTCF	chr5:98106000-98106150	GM12864	blood:	n/a	n/a
37	CTCF	chr5:98103564-98106247	A549	lung:	n/a	chr5:98104934-98104947 chr5:98104931-98104949 chr5:98104933-98104954
38	POLR2A	chr5:98103751-98106031	H1-hESC	embryonic stem cell:	n/a	n/a
39	CTCF	chr5:98105940-98106090	AoAF	blood vessel:	n/a	n/a
40	CTCF	chr5:98106020-98106170	HCPEpiC	choroid plexus:	n/a	n/a
41	POLR2A	chr5:98105942-98106590	H1-neurons	neurons:	n/a	n/a
42	CHD1	chr5:98103004-98112580	IMR90	lung:	n/a	chr5:98110353-98110363 chr5:98104638-98104648
43	SMARCB1	chr5:98105364-98106738	Hela-S3	cervix:	n/a	n/a
44	RAD21	chr5:98105743-98106070	A549	lung:	n/a	n/a
45	ELF1	chr5:98105768-98106401	GM12878	blood:	n/a	n/a
46	POLR2A	chr5:98104434-98106483	H1-neurons	neurons:	n/a	n/a
47	E2F4	chr5:98105987-98106182	MCF10A-Er-Src	breast:	n/a	n/a
48	MAX	chr5:98105938-98106839	HepG2	liver:	n/a	n/a
49	POLR2A	chr5:98105442-98106030	PANC-1	pancreas:	n/a	n/a
50	MXI1	chr5:98103700-98107724	IMR90	lung:	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	chr5:98102131..98106489-chr5:98107320..98111501,11	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CHD1-1	chr5:98105322-98106888	ENSG00000246763.2
2	lnc-CHD1-1	chr5:98105322-98106888	ENSG00000246763.2
3	lnc-CHD1-1	chr5:98105322-98106888	NR_033932

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

Extended variants
information (count: 12 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11242487	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12652843	0.98[ASN][1000 genomes]
rs12656672	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2545674	0.83[ASN][1000 genomes]
rs2662269	0.83[ASN][1000 genomes]
rs3849789	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3849790	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60106201	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61202875	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72773668	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72773670	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[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
rs2277929	RGMB	cis	normal skin	skin_eQTL
rs2277929	RGMB-AS1	cis	Thyroid	GTEx
rs2277929	RGMB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 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	chr5:98103800-98106200	Active TSS	Fetal Brain Female	brain
5	chr5:98103800-98107400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr5:98103800-98107400	Active TSS	Breast Myoepithelial Primary Cells	Breast
7	chr5:98103800-98107400	Flanking Active TSS	Liver	Liver
8	chr5:98103800-98107400	Active TSS	Brain Angular Gyrus	brain
9	chr5:98103800-98107400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
10	chr5:98103800-98107400	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr5:98103800-98107600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
12	chr5:98103800-98107800	Active TSS	Brain Cingulate Gyrus	brain
13	chr5:98103800-98108000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr5:98103800-98108000	Active TSS	Brain Inferior Temporal Lobe	brain
15	chr5:98103800-98108200	Active TSS	Fetal Kidney	kidney
16	chr5:98103800-98112600	Active TSS	Rectal Smooth Muscle	rectum
17	chr5:98104000-98106400	Active TSS	NHDF-Ad	bronchial
18	chr5:98104000-98106600	Active TSS	H9 Cell Line	embryonic stem cell
19	chr5:98104000-98106600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr5:98104000-98106600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
21	chr5:98104000-98107000	Active TSS	Stomach Mucosa	stomach
22	chr5:98104000-98107200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr5:98104000-98107200	Active TSS	Gastric	stomach
24	chr5:98104000-98107400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
25	chr5:98104000-98107400	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
26	chr5:98104000-98107400	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
27	chr5:98104000-98107400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr5:98104000-98107400	Active TSS	Brain Substantia Nigra	brain
29	chr5:98104000-98107400	Active TSS	Left Ventricle	heart
30	chr5:98104000-98107400	Active TSS	Ovary	ovary
31	chr5:98104000-98107400	Active TSS	Pancreas	Pancrea
32	chr5:98104000-98107600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
33	chr5:98104000-98107600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr5:98104000-98107600	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
35	chr5:98104000-98107600	Flanking Active TSS	Adipose Nuclei	Adipose
36	chr5:98104000-98107600	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
37	chr5:98104000-98107800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr5:98104000-98108200	Active TSS	Fetal Intestine Large	intestine
39	chr5:98104000-98111400	Active TSS	Psoas Muscle	Psoas
40	chr5:98104000-98113400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr5:98104200-98107400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr5:98104200-98108000	Active TSS	Brain Hippocampus Middle	brain
43	chr5:98104200-98111600	Active TSS	Right Atrium	heart
44	chr5:98104400-98106400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr5:98104400-98106600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
46	chr5:98104400-98107000	Active TSS	Small Intestine	intestine
47	chr5:98104400-98107400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr5:98104400-98107400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
49	chr5:98104400-98107400	Active TSS	Osteobl	bone
50	chr5:98104400-98107600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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