Variant report

Variant	rs327811
Chromosome Location	chr5:98271175-98271176
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:98269258..98271296-chr5:98288726..98290603,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RGMB-1	chr5:98270246-98271477	NONHSAT102972

Variant related genes	Relation type
ENSG00000241597	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs150991	0.84[AMR][1000 genomes]
rs150992	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs151102	0.87[CEU][hapmap];0.83[GIH][hapmap];0.81[MEX][hapmap];0.92[TSI][hapmap];0.87[EUR][1000 genomes]
rs161735	0.95[CEU][hapmap]
rs161740	0.95[CEU][hapmap];0.86[GIH][hapmap];0.90[TSI][hapmap]
rs161747	0.95[CEU][hapmap];0.86[GIH][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes]
rs161936	0.84[MEX][hapmap];0.81[TSI][hapmap]
rs161938	0.86[LWK][hapmap];0.82[MKK][hapmap]
rs161939	0.85[AMR][1000 genomes]
rs161941	0.89[LWK][hapmap];0.82[MKK][hapmap];0.83[TSI][hapmap];0.81[YRI][hapmap]
rs161948	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs161950	0.95[CEU][hapmap];0.86[GIH][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes]
rs161952	0.95[CEU][hapmap];0.86[GIH][hapmap];0.86[LWK][hapmap];0.90[TSI][hapmap];0.88[AMR][1000 genomes]
rs161953	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs161954	0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs161956	0.81[AMR][1000 genomes]
rs162140	0.81[YRI][hapmap]
rs162149	0.90[JPT][hapmap];0.85[AMR][1000 genomes]
rs162150	0.91[LWK][hapmap];0.83[MKK][hapmap];0.83[TSI][hapmap];0.81[YRI][hapmap];0.87[AMR][1000 genomes]
rs325200	0.81[AMR][1000 genomes]
rs325220	0.84[MEX][hapmap];0.88[TSI][hapmap]
rs326463	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs326464	0.85[AMR][1000 genomes]
rs326468	0.83[TSI][hapmap];0.85[AMR][1000 genomes]
rs326469	0.88[AMR][1000 genomes]
rs326480	0.87[CEU][hapmap];0.87[EUR][1000 genomes]
rs326481	0.82[JPT][hapmap]
rs327792	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs327793	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs327803	0.87[AMR][1000 genomes]
rs327807	0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs330419	0.95[CEU][hapmap];0.86[GIH][hapmap];0.91[LWK][hapmap];0.90[TSI][hapmap]
rs330421	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs330422	0.88[LWK][hapmap];0.83[TSI][hapmap]
rs331929	0.95[CEU][hapmap];0.82[JPT][hapmap]
rs34489	0.84[MEX][hapmap];0.81[TSI][hapmap]
rs34495	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs40075	0.84[MEX][hapmap];0.88[TSI][hapmap]
rs428836	0.86[EUR][1000 genomes]
rs466340	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs467728	0.87[CEU][hapmap];0.86[EUR][1000 genomes]
rs469018	0.81[EUR][1000 genomes]
rs6860504	0.81[YRI][hapmap]
rs692832	0.95[CEU][hapmap];0.85[GIH][hapmap];0.89[LWK][hapmap];0.90[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv882415	chr5:98134186-98312447	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv882416	chr5:98146106-98312447	Bivalent/Poised TSS Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv537818	chr5:98241627-98279192	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
4	nsv537819	chr5:98253348-98299646	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs327811	RGMB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:98266000-98272400	Weak transcription	Aorta	Aorta
2	chr5:98266000-98276400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr5:98266000-98276400	Weak transcription	Placenta	Placenta
4	chr5:98266200-98272600	Weak transcription	Fetal Muscle Leg	muscle
5	chr5:98266200-98273200	Weak transcription	Right Ventricle	heart
6	chr5:98266200-98274200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr5:98266200-98283600	Weak transcription	Colonic Mucosa	Colon
8	chr5:98266400-98271200	Enhancers	Primary T helper naive cells from peripheral blood	blood
9	chr5:98266400-98271400	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr5:98266400-98271400	Enhancers	Primary T killer memory cells from peripheral blood	blood
11	chr5:98266400-98272400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr5:98266400-98272600	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr5:98266400-98273000	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr5:98266400-98273400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr5:98266400-98273400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr5:98266400-98276200	Weak transcription	Fetal Kidney	kidney
17	chr5:98266600-98272000	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr5:98266600-98273400	Weak transcription	NHDF-Ad	bronchial
19	chr5:98266600-98291400	Weak transcription	Brain Germinal Matrix	brain
20	chr5:98266800-98273200	Weak transcription	HUVEC	blood vessel
21	chr5:98266800-98274000	Weak transcription	Fetal Lung	lung
22	chr5:98266800-98277000	Weak transcription	HMEC	breast
23	chr5:98266800-98278400	Weak transcription	Hela-S3	cervix
24	chr5:98266800-98283200	Weak transcription	Duodenum Mucosa	Duodenum
25	chr5:98267000-98274000	Weak transcription	Adipose Nuclei	Adipose
26	chr5:98267200-98272400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr5:98267400-98271400	Enhancers	Primary B cells from peripheral blood	blood
28	chr5:98267400-98272600	Weak transcription	Fetal Intestine Small	intestine
29	chr5:98267400-98277800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr5:98268600-98271400	Enhancers	Brain Anterior Caudate	brain
31	chr5:98268600-98271400	Enhancers	Brain Cingulate Gyrus	brain
32	chr5:98269000-98271400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr5:98269400-98273400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
34	chr5:98269600-98271200	Weak transcription	Pancreas	Pancrea
35	chr5:98269600-98271400	Enhancers	Primary T helper cells PMA-I stimulated	--
36	chr5:98269600-98271400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
37	chr5:98269600-98272000	Enhancers	Cortex derived primary cultured neurospheres	brain
38	chr5:98269600-98272400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr5:98269600-98274200	Weak transcription	Stomach Smooth Muscle	stomach
40	chr5:98269600-98274200	Weak transcription	Thymus	Thymus
41	chr5:98269600-98274400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr5:98269600-98274600	Weak transcription	Right Atrium	heart
43	chr5:98269800-98271600	Enhancers	Primary B cells from cord blood	blood
44	chr5:98269800-98274200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr5:98270000-98275600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr5:98270200-98271200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr5:98270200-98271200	Enhancers	Primary neutrophils fromperipheralblood	blood
48	chr5:98270200-98271400	Enhancers	Osteobl	bone
49	chr5:98270200-98271600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr5:98270200-98271600	Enhancers	Brain Hippocampus Middle	brain

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