Variant report

Variant	rs1002952
Chromosome Location	chr5:98114140-98114141
allele	A/G
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	CHD1	chr5:98113963-98115956	IMR90	lung:	n/a	n/a
2	STAT3	chr5:98114094-98114245	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
RGMB-AS1	TF binding region
RGMB	TF binding region

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1002859	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1508792	0.92[ASN][1000 genomes]
rs1508793	0.92[ASN][1000 genomes]
rs1818348	0.82[ASN][1000 genomes]
rs1828169	0.82[ASN][1000 genomes]
rs1979980	0.82[ASN][1000 genomes]
rs2249797	0.82[ASN][1000 genomes]
rs2250807	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2545676	0.97[ASN][1000 genomes]
rs2545732	0.83[ASN][1000 genomes]
rs2547973	0.86[ASN][1000 genomes]
rs331550	0.97[ASN][1000 genomes]
rs331551	0.84[ASN][1000 genomes]
rs331552	0.97[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1002952	RGMB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:98109600-98119200	Transcr. at gene 5' and 3'	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr5:98109800-98114600	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
3	chr5:98110200-98125200	Transcr. at gene 5' and 3'	NHDF-Ad	bronchial
4	chr5:98110400-98119200	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr5:98110600-98115200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr5:98110800-98115200	Weak transcription	Lung	lung
7	chr5:98110800-98118600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr5:98110800-98123200	Weak transcription	Aorta	Aorta
9	chr5:98111000-98115200	Weak transcription	Esophagus	oesophagus
10	chr5:98111000-98116200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr5:98111000-98118600	Weak transcription	Gastric	stomach
12	chr5:98111000-98128800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr5:98111000-98131800	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr5:98111600-98116000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr5:98111600-98131800	Weak transcription	Placenta	Placenta
16	chr5:98111800-98114600	Weak transcription	Stomach Mucosa	stomach
17	chr5:98111800-98115200	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr5:98111800-98116200	Weak transcription	Fetal Kidney	kidney
19	chr5:98111800-98119000	Weak transcription	Spleen	Spleen
20	chr5:98111800-98120200	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr5:98112000-98114600	Weak transcription	Liver	Liver
22	chr5:98112000-98115000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr5:98112000-98115400	Weak transcription	Primary B cells from peripheral blood	blood
24	chr5:98112000-98115400	Weak transcription	Brain Substantia Nigra	brain
25	chr5:98112000-98116200	Weak transcription	A549	lung
26	chr5:98112000-98135800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr5:98112200-98114600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr5:98112200-98114600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr5:98112200-98115000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr5:98112200-98115200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr5:98112200-98115200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr5:98112200-98117600	Strong transcription	HUES64 Cell Line	embryonic stem cell
33	chr5:98112200-98118800	Weak transcription	Brain Angular Gyrus	brain
34	chr5:98112400-98114200	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr5:98112400-98114200	Active TSS	NHLF	lung
36	chr5:98112400-98115000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr5:98112400-98115000	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr5:98112400-98115000	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr5:98112400-98115000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr5:98112400-98115000	Weak transcription	Adipose Nuclei	Adipose
41	chr5:98112400-98115000	Weak transcription	HMEC	breast
42	chr5:98112400-98115200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr5:98112400-98115200	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr5:98112400-98115200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr5:98112400-98115200	Weak transcription	Brain Cingulate Gyrus	brain
46	chr5:98112400-98115200	Weak transcription	Brain Germinal Matrix	brain
47	chr5:98112400-98115200	Weak transcription	Colonic Mucosa	Colon
48	chr5:98112400-98115200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr5:98112400-98115200	Weak transcription	Fetal Lung	lung
50	chr5:98112400-98115200	Weak transcription	Right Atrium	heart

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