Variant report

Variant	rs6557009
Chromosome Location	chr5:97174928-97174929
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 87 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs11135531	0.85[CEU][hapmap]
rs11135532	0.85[CEU][hapmap]
rs12653428	0.97[ASN][1000 genomes]
rs12654021	0.97[ASN][1000 genomes]
rs12655508	0.97[ASN][1000 genomes]
rs12655548	0.97[ASN][1000 genomes]
rs12656172	0.97[ASN][1000 genomes]
rs4327612	0.97[ASN][1000 genomes]
rs4379225	0.97[ASN][1000 genomes]
rs4440387	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4551099	0.93[ASN][1000 genomes]
rs55706044	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs55725155	0.94[EUR][1000 genomes]
rs55743944	0.97[ASN][1000 genomes]
rs55817884	0.94[EUR][1000 genomes]
rs55937002	0.97[ASN][1000 genomes]
rs56074649	0.97[ASN][1000 genomes]
rs56152369	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56260839	0.96[EUR][1000 genomes]
rs56313368	0.97[ASN][1000 genomes]
rs56336851	0.97[ASN][1000 genomes]
rs56666656	0.97[ASN][1000 genomes]
rs58700659	0.91[EUR][1000 genomes]
rs59931467	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61166915	0.97[ASN][1000 genomes]
rs61545180	0.97[ASN][1000 genomes]
rs6557011	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs66476007	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs66774764	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs67435821	0.89[EUR][1000 genomes]
rs67922319	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs67935527	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs68166390	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6859489	0.89[EUR][1000 genomes]
rs6882744	1.00[ASN][1000 genomes]
rs6884205	0.89[EUR][1000 genomes]
rs6890322	0.97[ASN][1000 genomes]
rs72779661	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72779662	0.97[ASN][1000 genomes]
rs72779664	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72779665	0.97[ASN][1000 genomes]
rs72779667	0.97[ASN][1000 genomes]
rs72779669	0.97[ASN][1000 genomes]
rs72779670	0.97[ASN][1000 genomes]
rs72779671	0.97[ASN][1000 genomes]
rs72779673	0.97[ASN][1000 genomes]
rs72779675	0.97[ASN][1000 genomes]
rs72779676	0.97[ASN][1000 genomes]
rs72779677	0.97[ASN][1000 genomes]
rs72779680	0.97[ASN][1000 genomes]
rs72779683	0.97[ASN][1000 genomes]
rs72779685	0.97[ASN][1000 genomes]
rs72779686	0.97[ASN][1000 genomes]
rs72779690	0.97[ASN][1000 genomes]
rs72779691	0.97[ASN][1000 genomes]
rs72781505	0.97[ASN][1000 genomes]
rs72781506	0.97[ASN][1000 genomes]
rs72781508	0.97[ASN][1000 genomes]
rs72781509	0.97[ASN][1000 genomes]
rs72781511	0.97[ASN][1000 genomes]
rs72781512	0.97[ASN][1000 genomes]
rs72781514	0.97[ASN][1000 genomes]
rs72781515	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72781520	0.97[ASN][1000 genomes]
rs72781522	0.97[ASN][1000 genomes]
rs72781524	0.97[ASN][1000 genomes]
rs72781525	0.97[ASN][1000 genomes]
rs72781527	0.97[ASN][1000 genomes]
rs7701490	0.97[ASN][1000 genomes]
rs7714125	0.97[ASN][1000 genomes]
rs7715312	0.85[CEU][hapmap];0.89[GIH][hapmap]
rs7719818	0.97[ASN][1000 genomes]
rs7724005	0.97[ASN][1000 genomes]
rs7729626	0.97[ASN][1000 genomes]
rs7732992	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534326	chr5:96531217-97283481	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv1031429	chr5:96777286-97269498	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv527650	chr5:96783726-97260358	Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1028224	chr5:96791214-97258383	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv537814	chr5:96791214-97258383	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1020125	chr5:96937248-97350644	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv432757	chr5:97006304-97213768	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	esv2754965	chr5:97013452-97296147	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv1027714	chr5:97034552-97211333	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv471024	chr5:97048466-97187183	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	nsv1034347	chr5:97062961-97241450	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv830418	chr5:97139371-97326878	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6557009	RGMB	cis	parietal	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:97173600-97175800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr5:97173600-97175800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr5:97173600-97176800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr5:97173600-97176800	Enhancers	Hela-S3	cervix
5	chr5:97173600-97176800	Enhancers	HSMM	muscle
6	chr5:97173600-97176800	Enhancers	NH-A	brain
7	chr5:97173600-97176800	Enhancers	NHDF-Ad	bronchial
8	chr5:97173600-97177000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr5:97173600-97177000	Enhancers	Osteobl	bone
10	chr5:97173800-97175400	Enhancers	Duodenum Mucosa	Duodenum
11	chr5:97173800-97175400	Enhancers	HSMMtube	muscle
12	chr5:97173800-97175600	Enhancers	Dnd41	blood
13	chr5:97173800-97176600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr5:97173800-97176600	Enhancers	Adipose Nuclei	Adipose
15	chr5:97173800-97176600	Enhancers	NHEK	skin
16	chr5:97173800-97176600	Enhancers	NHLF	lung
17	chr5:97173800-97176800	Enhancers	Fetal Lung	lung
18	chr5:97173800-97176800	Enhancers	HMEC	breast
19	chr5:97174000-97177000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr5:97174000-97177400	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr5:97174200-97175200	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr5:97174200-97175800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr5:97174200-97176400	Weak transcription	Ovary	ovary
24	chr5:97174200-97176800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr5:97174400-97175000	Flanking Active TSS	HUVEC	blood vessel
26	chr5:97174400-97175200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr5:97174400-97175400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr5:97174400-97175400	Enhancers	Duodenum Smooth Muscle	Duodenum
29	chr5:97174400-97176800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr5:97174400-97176800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr5:97174600-97176600	Weak transcription	Colon Smooth Muscle	Colon
32	chr5:97174600-97177000	Enhancers	Muscle Satellite Cultured Cells	--
33	chr5:97174800-97175200	Enhancers	Fetal Muscle Leg	muscle
34	chr5:97174800-97175800	Enhancers	Fetal Stomach	stomach

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