Variant report

Variant	rs2617508
Chromosome Location	chr5:98130968-98130969
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:98129808..98132282-chr5:98134081..98135788,2	K562	blood:
2	chr5:98123018..98126275-chr5:98130087..98132367,4	MCF-7	breast:
3	chr5:98105450..98112138-chr5:98128603..98138411,14	MCF-7	breast:
4	chr5:98124398..98126468-chr5:98128299..98131960,3	MCF-7	breast:
5	chr5:98126420..98128371-chr5:98130230..98131989,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000174136	Chromatin interaction
ENSG00000246763	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10515283	1.00[ASN][1000 genomes]
rs1828168	1.00[ASN][1000 genomes]
rs2545677	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2545680	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2545688	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2545727	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2545728	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2545729	0.98[EUR][1000 genomes]
rs2617512	0.97[EUR][1000 genomes]
rs2617515	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2662255	0.98[EUR][1000 genomes]
rs2662256	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2662259	0.98[EUR][1000 genomes]
rs2662260	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2662261	0.98[EUR][1000 genomes]
rs2859485	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72773677	1.00[ASN][1000 genomes]
rs72773692	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72773694	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2617508	RGMB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:98111000-98131800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr5:98111600-98131800	Weak transcription	Placenta	Placenta
3	chr5:98112000-98135800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr5:98114800-98131400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr5:98117600-98132200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr5:98118400-98131800	Weak transcription	A549	lung
7	chr5:98122200-98132000	Weak transcription	Brain Cingulate Gyrus	brain
8	chr5:98123000-98132400	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr5:98123800-98131000	Weak transcription	Right Atrium	heart
10	chr5:98123800-98132000	Weak transcription	Primary T cells from cord blood	blood
11	chr5:98123800-98136800	Weak transcription	Fetal Brain Male	brain
12	chr5:98123800-98140600	Weak transcription	Brain Substantia Nigra	brain
13	chr5:98124000-98132000	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr5:98124000-98132000	Weak transcription	Fetal Lung	lung
15	chr5:98125200-98132000	Genic enhancers	NHDF-Ad	bronchial
16	chr5:98125600-98132000	Weak transcription	Stomach Mucosa	stomach
17	chr5:98126200-98131200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr5:98127400-98131200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr5:98127400-98131600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr5:98127600-98131600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr5:98127600-98131800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr5:98127600-98131800	Weak transcription	Fetal Kidney	kidney
23	chr5:98127800-98131200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr5:98127800-98131800	Weak transcription	Colon Smooth Muscle	Colon
25	chr5:98128000-98131000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr5:98128600-98131200	Strong transcription	Fetal Intestine Small	intestine
27	chr5:98128600-98131400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr5:98128800-98131000	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr5:98128800-98131200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr5:98128800-98131200	Strong transcription	Fetal Brain Female	brain
31	chr5:98129000-98131400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr5:98129200-98131200	Genic enhancers	Osteobl	bone
33	chr5:98129200-98131600	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr5:98129200-98132200	Weak transcription	Hela-S3	cervix
35	chr5:98129400-98131000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr5:98129400-98131000	Weak transcription	Brain Angular Gyrus	brain
37	chr5:98129400-98131000	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr5:98129400-98131000	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr5:98129400-98131200	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr5:98129400-98131200	Strong transcription	Fetal Muscle Trunk	muscle
41	chr5:98129400-98131400	Weak transcription	Duodenum Mucosa	Duodenum
42	chr5:98129400-98131600	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr5:98129400-98131600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr5:98129400-98131600	Weak transcription	Left Ventricle	heart
45	chr5:98129400-98131600	Weak transcription	Pancreas	Pancrea
46	chr5:98129400-98131800	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr5:98129400-98131800	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr5:98129400-98131800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr5:98129400-98132000	Weak transcription	Spleen	Spleen
50	chr5:98129400-98132200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links