Variant report

Variant	rs2545676
Chromosome Location	chr5:98113923-98113924
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1002859	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1002952	0.97[ASN][1000 genomes]
rs13541	0.84[CHB][hapmap]
rs1508792	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1508793	0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1818348	0.83[ASN][1000 genomes]
rs1828169	0.94[CHB][hapmap];0.83[ASN][1000 genomes]
rs1911904	0.84[CHB][hapmap]
rs1979980	0.94[CHB][hapmap];0.83[ASN][1000 genomes]
rs2249797	0.83[ASN][1000 genomes]
rs2250807	1.00[CHB][hapmap];0.93[JPT][hapmap];0.97[ASN][1000 genomes]
rs2545673	0.84[CHB][hapmap]
rs2545730	0.80[ASN][1000 genomes]
rs2545732	0.84[ASN][1000 genomes]
rs2547973	0.83[ASN][1000 genomes]
rs2662258	0.96[CEU][hapmap];0.90[CHB][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2662264	0.84[CHB][hapmap]
rs331550	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs331551	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs331552	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs970079	0.96[CEU][hapmap];0.95[CHB][hapmap];0.92[AMR][1000 genomes];0.95[EUR][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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2545676	RGMB	cis	multi-tissue	Pritchard
rs2545676	RGMB	cis	uninvolved skin	skin_eQTL
rs2545676	RGMB	Cis_1M	lymphoblastoid	RTeQTL
rs2545676	RGMB	cis	normal skin	skin_eQTL

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	chr5:98111800-98114000	Enhancers	Primary T helper cells PMA-I stimulated	--
17	chr5:98111800-98114600	Weak transcription	Stomach Mucosa	stomach
18	chr5:98111800-98115200	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr5:98111800-98116200	Weak transcription	Fetal Kidney	kidney
20	chr5:98111800-98119000	Weak transcription	Spleen	Spleen
21	chr5:98111800-98120200	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr5:98112000-98114600	Weak transcription	Liver	Liver
23	chr5:98112000-98115000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr5:98112000-98115400	Weak transcription	Primary B cells from peripheral blood	blood
25	chr5:98112000-98115400	Weak transcription	Brain Substantia Nigra	brain
26	chr5:98112000-98116200	Weak transcription	A549	lung
27	chr5:98112000-98135800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr5:98112200-98114600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr5:98112200-98114600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr5:98112200-98115000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr5:98112200-98115200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr5:98112200-98115200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr5:98112200-98117600	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr5:98112200-98118800	Weak transcription	Brain Angular Gyrus	brain
35	chr5:98112400-98114200	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr5:98112400-98114200	Active TSS	NHLF	lung
37	chr5:98112400-98115000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr5:98112400-98115000	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr5:98112400-98115000	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr5:98112400-98115000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr5:98112400-98115000	Weak transcription	Adipose Nuclei	Adipose
42	chr5:98112400-98115000	Weak transcription	HMEC	breast
43	chr5:98112400-98115200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr5:98112400-98115200	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr5:98112400-98115200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr5:98112400-98115200	Weak transcription	Brain Cingulate Gyrus	brain
47	chr5:98112400-98115200	Weak transcription	Brain Germinal Matrix	brain
48	chr5:98112400-98115200	Weak transcription	Colonic Mucosa	Colon
49	chr5:98112400-98115200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr5:98112400-98115200	Weak transcription	Fetal Lung	lung

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