Variant report

Variant	rs331551
Chromosome Location	chr5:98117707-98117708
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1002859	0.95[CHB][hapmap];0.91[CHD][hapmap];0.84[ASN][1000 genomes]
rs1002952	0.84[ASN][1000 genomes]
rs13541	0.85[CHB][hapmap];0.89[CHD][hapmap]
rs1508792	0.90[CHB][hapmap]
rs1508793	0.90[CHB][hapmap];0.91[CHD][hapmap]
rs161937	0.87[ASW][hapmap]
rs1818348	0.87[ASN][1000 genomes]
rs1828169	0.90[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.85[TSI][hapmap];0.87[ASN][1000 genomes]
rs1911904	0.81[CHB][hapmap];0.86[CHD][hapmap];0.84[GIH][hapmap];0.84[JPT][hapmap];0.82[TSI][hapmap]
rs1979980	0.90[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs2249797	0.86[ASN][1000 genomes]
rs2250807	0.94[CHB][hapmap];0.84[ASN][1000 genomes]
rs2545673	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs2545675	0.83[ASN][1000 genomes]
rs2545676	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2545730	0.85[ASN][1000 genomes]
rs2545731	0.84[ASN][1000 genomes]
rs2547972	0.84[ASN][1000 genomes]
rs2662258	1.00[ASW][hapmap];0.96[CEU][hapmap];0.86[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2662264	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs331550	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs331552	0.96[CEU][hapmap];0.95[CHB][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs692759	0.87[ASW][hapmap]
rs970079	0.96[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs331551	RGMB	Cis_1M	lymphoblastoid	RTeQTL
rs331551	RGMB	cis	multi-tissue	Pritchard
rs331551	RGMB	cis	normal skin	skin_eQTL
rs331551	RGMB	cis	uninvolved skin	skin_eQTL
rs331551	RGMB	cis	Liver	GTEx

Chromatin state (count:111 , 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	chr5:98110200-98125200	Transcr. at gene 5' and 3'	NHDF-Ad	bronchial
3	chr5:98110400-98119200	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr5:98110800-98118600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr5:98110800-98123200	Weak transcription	Aorta	Aorta
6	chr5:98111000-98118600	Weak transcription	Gastric	stomach
7	chr5:98111000-98128800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr5:98111000-98131800	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr5:98111600-98131800	Weak transcription	Placenta	Placenta
10	chr5:98111800-98119000	Weak transcription	Spleen	Spleen
11	chr5:98111800-98120200	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr5:98112000-98135800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr5:98112200-98118800	Weak transcription	Brain Angular Gyrus	brain
14	chr5:98112400-98118200	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr5:98112400-98120400	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr5:98112400-98121600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr5:98112400-98122400	Weak transcription	Fetal Heart	heart
18	chr5:98113000-98118200	Weak transcription	Brain Anterior Caudate	brain
19	chr5:98113200-98120000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr5:98113400-98118200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr5:98113400-98120000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr5:98113400-98120800	Weak transcription	Fetal Brain Male	brain
23	chr5:98114000-98120200	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr5:98114600-98117800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr5:98114600-98119800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
26	chr5:98114600-98120800	Genic enhancers	Muscle Satellite Cultured Cells	--
27	chr5:98114800-98131400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr5:98115000-98118000	Strong transcription	HMEC	breast
29	chr5:98115000-98118600	Strong transcription	Cortex derived primary cultured neurospheres	brain
30	chr5:98115000-98118800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr5:98115000-98122200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr5:98115000-98125400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr5:98115200-98119000	Strong transcription	H1 Cell Line	embryonic stem cell
34	chr5:98115200-98119200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
35	chr5:98115200-98119800	Strong transcription	HUES48 Cell Line	embryonic stem cell
36	chr5:98115200-98120200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
37	chr5:98115200-98120200	Strong transcription	HSMMtube	muscle
38	chr5:98115200-98120600	Genic enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr5:98115400-98118600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr5:98115600-98117800	Weak transcription	Esophagus	oesophagus
41	chr5:98115600-98117800	Weak transcription	Psoas Muscle	Psoas
42	chr5:98115600-98118000	Strong transcription	Adipose Nuclei	Adipose
43	chr5:98115600-98118000	Strong transcription	Fetal Lung	lung
44	chr5:98115600-98118400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr5:98115600-98119800	Weak transcription	Colonic Mucosa	Colon
46	chr5:98115600-98119800	Strong transcription	NH-A	brain
47	chr5:98115600-98121200	Weak transcription	Primary T cells fromperipheralblood	blood
48	chr5:98115600-98121400	Strong transcription	Fetal Muscle Trunk	muscle
49	chr5:98115600-98123200	Weak transcription	Primary T cells from cord blood	blood
50	chr5:98115800-98117800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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