Variant report

Variant	rs469519
Chromosome Location	chr5:98241065-98241066
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:98232177..98234345-chr5:98238725..98241522,2	K562	blood:
2	chr5:98238981..98243002-chr5:98262998..98267488,6	MCF-7	breast:
3	chr5:98240910..98242219-chr5:98367905..98368817,11	MCF-7	breast:
4	chr5:98239512..98242254-chr5:98395636..98397336,2	K562	blood:

Variant related genes	Relation type
ENSG00000248489	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs150935	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs152034	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs161729	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs161730	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs161734	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161736	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161737	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161738	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161739	0.88[CEU][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161744	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161745	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161746	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs161749	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs161750	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161940	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs161945	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161947	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs161957	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs167798	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2447826	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2545733	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2545734	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2545735	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2545736	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2545737	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2545738	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2545739	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2545740	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2578576	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2578577	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2617514	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs325195	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs325199	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs325203	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs325204	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs325208	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs325209	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs325214	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs326487	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs331541	0.86[EUR][1000 genomes]
rs331542	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs331544	0.86[EUR][1000 genomes]
rs331548	0.85[EUR][1000 genomes]
rs331927	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs331928	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34488	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs992774	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs469519	RGMB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:98188400-98247000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr5:98189800-98241400	Strong transcription	HUES64 Cell Line	embryonic stem cell
3	chr5:98189800-98241400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
4	chr5:98189800-98241800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr5:98190400-98241200	Strong transcription	Fetal Thymus	thymus
6	chr5:98190400-98243800	Strong transcription	Dnd41	blood
7	chr5:98200000-98263000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr5:98211400-98241200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr5:98215000-98263000	Weak transcription	Esophagus	oesophagus
10	chr5:98216800-98241400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr5:98222000-98247000	Weak transcription	Fetal Heart	heart
12	chr5:98225800-98258400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr5:98228200-98259200	Weak transcription	Spleen	Spleen
14	chr5:98228400-98259200	Weak transcription	Gastric	stomach
15	chr5:98228400-98259400	Weak transcription	Brain Cingulate Gyrus	brain
16	chr5:98228400-98263000	Weak transcription	Aorta	Aorta
17	chr5:98232000-98243800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr5:98232000-98247000	Weak transcription	Right Ventricle	heart
19	chr5:98232000-98254200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr5:98232000-98258200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr5:98232000-98259200	Weak transcription	Pancreas	Pancrea
22	chr5:98233600-98245200	Weak transcription	Brain Hippocampus Middle	brain
23	chr5:98235000-98247000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr5:98235000-98262600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr5:98235200-98261600	Weak transcription	Fetal Kidney	kidney
26	chr5:98235400-98262600	Weak transcription	Fetal Brain Male	brain
27	chr5:98236000-98241600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr5:98236000-98256800	Weak transcription	Rectal Smooth Muscle	rectum
29	chr5:98236400-98256600	Weak transcription	Lung	lung
30	chr5:98236400-98258400	Weak transcription	Brain Germinal Matrix	brain
31	chr5:98236400-98263200	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr5:98236600-98243800	Weak transcription	Thymus	Thymus
33	chr5:98236600-98247000	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr5:98236600-98248000	Weak transcription	Fetal Intestine Small	intestine
35	chr5:98236600-98248000	Weak transcription	Fetal Stomach	stomach
36	chr5:98236600-98249600	Weak transcription	Psoas Muscle	Psoas
37	chr5:98236600-98257600	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr5:98236600-98259000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr5:98236600-98261000	Weak transcription	Small Intestine	intestine
40	chr5:98236600-98261600	Weak transcription	Fetal Brain Female	brain
41	chr5:98236600-98263000	Weak transcription	Ovary	ovary
42	chr5:98236800-98246400	Weak transcription	Brain Anterior Caudate	brain
43	chr5:98236800-98247000	Weak transcription	Brain Angular Gyrus	brain
44	chr5:98236800-98248000	Weak transcription	Fetal Muscle Trunk	muscle
45	chr5:98236800-98249800	Weak transcription	Stomach Smooth Muscle	stomach
46	chr5:98236800-98253600	Weak transcription	Left Ventricle	heart
47	chr5:98236800-98254000	Weak transcription	Fetal Muscle Leg	muscle
48	chr5:98236800-98256000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr5:98236800-98263000	Weak transcription	Brain Substantia Nigra	brain
50	chr5:98237000-98245200	Weak transcription	Colon Smooth Muscle	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links