Variant report

Variant	rs2662261
Chromosome Location	chr5:98120138-98120139
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	chr5:98117951..98120530-chr5:98132324..98136136,3	MCF-7	breast:
2	chr5:98118498..98120988-chr5:98126962..98129374,2	MCF-7	breast:

Extended variants
information (count: 29 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1069182	0.85[ASN][1000 genomes]
rs162473	0.85[ASN][1000 genomes]
rs162611	0.85[ASN][1000 genomes]
rs170734	0.85[ASN][1000 genomes]
rs193072	0.85[ASN][1000 genomes]
rs2545677	0.91[EUR][1000 genomes]
rs2545680	0.91[EUR][1000 genomes]
rs2545688	0.91[EUR][1000 genomes]
rs2545727	0.92[EUR][1000 genomes]
rs2545728	0.91[EUR][1000 genomes]
rs2545729	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2545735	0.82[JPT][hapmap]
rs2617508	0.98[EUR][1000 genomes]
rs2617512	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2617515	0.91[EUR][1000 genomes]
rs2662255	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2662256	0.91[EUR][1000 genomes]
rs2662259	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2662260	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs2859485	0.91[EUR][1000 genomes]
rs331543	0.85[ASN][1000 genomes]
rs331545	0.85[ASN][1000 genomes]
rs331549	0.85[ASN][1000 genomes]
rs331918	0.85[ASN][1000 genomes]
rs72773692	0.91[EUR][1000 genomes]
rs72773694	0.91[EUR][1000 genomes]
rs992773	0.85[ASN][1000 genomes]
rs992775	0.85[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2662261	RGMB	Cis_1M	lymphoblastoid	RTeQTL
rs2662261	RGMB	cis	uninvolved skin	skin_eQTL
rs2662261	RGMB	cis	normal skin	skin_eQTL
rs2662261	RGMB	cis	lesional skin	skin_eQTL

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:98110200-98125200	Transcr. at gene 5' and 3'	NHDF-Ad	bronchial
2	chr5:98110800-98123200	Weak transcription	Aorta	Aorta
3	chr5:98111000-98128800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr5:98111000-98131800	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr5:98111600-98131800	Weak transcription	Placenta	Placenta
6	chr5:98111800-98120200	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr5:98112000-98135800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr5:98112400-98120400	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr5:98112400-98121600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr5:98112400-98122400	Weak transcription	Fetal Heart	heart
11	chr5:98113400-98120800	Weak transcription	Fetal Brain Male	brain
12	chr5:98114000-98120200	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr5:98114600-98120800	Genic enhancers	Muscle Satellite Cultured Cells	--
14	chr5:98114800-98131400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr5:98115000-98122200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr5:98115000-98125400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr5:98115200-98120200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
18	chr5:98115200-98120200	Strong transcription	HSMMtube	muscle
19	chr5:98115200-98120600	Genic enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr5:98115600-98121200	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr5:98115600-98121400	Strong transcription	Fetal Muscle Trunk	muscle
22	chr5:98115600-98123200	Weak transcription	Primary T cells from cord blood	blood
23	chr5:98115800-98120400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr5:98115800-98123200	Weak transcription	Right Atrium	heart
25	chr5:98115800-98123800	Genic enhancers	NHEK	skin
26	chr5:98116000-98120600	Strong transcription	HUVEC	blood vessel
27	chr5:98116200-98122000	Weak transcription	Primary B cells from cord blood	blood
28	chr5:98116400-98120200	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr5:98116600-98120400	Weak transcription	Fetal Kidney	kidney
30	chr5:98116600-98120800	Weak transcription	Rectal Smooth Muscle	rectum
31	chr5:98116600-98125200	Genic enhancers	Osteobl	bone
32	chr5:98116800-98123200	Weak transcription	HepG2	liver
33	chr5:98116800-98127600	Weak transcription	Hela-S3	cervix
34	chr5:98117000-98120200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr5:98117000-98120800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr5:98117000-98128600	Weak transcription	Primary T helper cells fromperipheralblood	blood
37	chr5:98117200-98121000	Genic enhancers	NHLF	lung
38	chr5:98117400-98120200	Weak transcription	Primary B cells from peripheral blood	blood
39	chr5:98117400-98121800	Enhancers	Duodenum Smooth Muscle	Duodenum
40	chr5:98117600-98132200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
41	chr5:98117800-98120200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr5:98117800-98120400	Genic enhancers	Rectal Mucosa Donor 31	rectum
43	chr5:98117800-98120800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr5:98117800-98121200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr5:98117800-98121400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr5:98117800-98125000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr5:98117800-98125200	Genic enhancers	Fetal Muscle Leg	muscle
48	chr5:98117800-98125600	Enhancers	Breast Myoepithelial Primary Cells	Breast
49	chr5:98117800-98128000	Genic enhancers	HSMM	muscle
50	chr5:98118000-98120200	Weak transcription	Adipose Nuclei	Adipose

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