Variant report

Variant	rs1393210
Chromosome Location	chr5:98361596-98361597
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:98263646..98265342-chr5:98360622..98362324,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000248489	Chromatin interaction

Extended variants
information (count: 94 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs10037147	0.84[EUR][1000 genomes]
rs10038192	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10040066	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10041261	0.94[ASN][1000 genomes]
rs10050423	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10076291	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10479344	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10479345	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10479346	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10479348	0.92[ASN][1000 genomes]
rs1093794	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1104262	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11242567	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11242574	1.00[ASN][1000 genomes]
rs11745405	1.00[ASN][1000 genomes]
rs11949103	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11950452	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11950855	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11960896	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12109067	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12189335	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12515042	1.00[ASN][1000 genomes]
rs13179812	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1472622	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1604450	1.00[ASN][1000 genomes]
rs161731	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs161935	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs161936	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs162341	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs172874	0.84[EUR][1000 genomes]
rs1875529	1.00[ASN][1000 genomes]
rs2221268	0.94[ASN][1000 genomes]
rs2455423	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2927647	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2927648	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2927654	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2937706	0.86[EUR][1000 genomes]
rs2937708	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2937709	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs325220	0.84[EUR][1000 genomes]
rs326493	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs327807	0.83[EUR][1000 genomes]
rs34489	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34490	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34491	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34496	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34497	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34499	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs363929	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs366000	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs366353	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs370529	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs378089	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs380156	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs393697	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs395668	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs398436	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs40075	0.83[EUR][1000 genomes]
rs407562	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs416750	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs422127	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs434039	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4343864	0.90[ASN][1000 genomes]
rs443726	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4448016	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs447044	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs449204	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs451141	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4565239	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4583911	1.00[ASN][1000 genomes]
rs45931	0.84[EUR][1000 genomes]
rs469018	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4703048	0.85[EUR][1000 genomes]
rs4703049	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4703051	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4703052	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4703340	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4703345	0.94[ASN][1000 genomes]
rs539024	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs559574	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6865618	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6878136	0.94[ASN][1000 genomes]
rs6885458	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs709390	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7710032	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7711061	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7712408	0.89[ASN][1000 genomes]
rs7719562	1.00[ASN][1000 genomes]
rs7719649	1.00[ASN][1000 genomes]
rs7723242	0.94[ASN][1000 genomes]
rs819232	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024391	chr5:98355665-98653657	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
2	nsv599118	chr5:98358191-99029453	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv599119	chr5:98358191-99315677	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1393210	RGMB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:98353600-98361600	Weak transcription	Small Intestine	intestine
2	chr5:98356400-98361600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr5:98356400-98361800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr5:98356400-98362400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr5:98357000-98362000	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr5:98357400-98368400	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr5:98358200-98366800	Weak transcription	K562	blood
8	chr5:98360000-98361800	Enhancers	Sigmoid Colon	Sigmoid Colon
9	chr5:98360000-98363200	Enhancers	Fetal Intestine Large	intestine
10	chr5:98360000-98363200	Enhancers	HepG2	liver
11	chr5:98360000-98363400	Enhancers	Stomach Mucosa	stomach
12	chr5:98360200-98362800	Enhancers	Duodenum Mucosa	Duodenum
13	chr5:98360200-98362800	Enhancers	Pancreas	Pancrea
14	chr5:98360200-98363400	Enhancers	Fetal Intestine Small	intestine
15	chr5:98360200-98369000	Enhancers	Primary B cells from peripheral blood	blood
16	chr5:98360400-98362200	Enhancers	GM12878-XiMat	blood
17	chr5:98360400-98362800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr5:98360600-98362000	Enhancers	Colonic Mucosa	Colon
19	chr5:98360600-98362400	Enhancers	Primary B cells from cord blood	blood
20	chr5:98360800-98363000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr5:98361000-98361600	Flanking Active TSS	A549	lung
22	chr5:98361000-98361800	Enhancers	Primary neutrophils fromperipheralblood	blood
23	chr5:98361000-98362600	Enhancers	Primary hematopoietic stem cells	blood
24	chr5:98361000-98362600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr5:98361000-98362800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr5:98361000-98363000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr5:98361200-98361600	Enhancers	Fetal Kidney	kidney
28	chr5:98361200-98361600	Enhancers	Fetal Stomach	stomach
29	chr5:98361200-98361800	Flanking Active TSS	Liver	Liver
30	chr5:98361200-98361800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
31	chr5:98361200-98362400	Enhancers	Primary hematopoietic stem cells short term culture	blood
32	chr5:98361200-98362600	Enhancers	Dnd41	blood
33	chr5:98361200-98363000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr5:98361200-98363600	Enhancers	Adipose Nuclei	Adipose
35	chr5:98361200-98364400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
36	chr5:98361200-98368000	Weak transcription	Osteobl	bone
37	chr5:98361400-98361600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
38	chr5:98361400-98361800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr5:98361400-98361800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
40	chr5:98361400-98362400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr5:98361400-98363000	Weak transcription	ES-I3 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links