Variant report

Variant	rs13101237
Chromosome Location	chr3:99219235-99219236
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-COL8A1-2	chr3:99219191-99219385	XLOC_002737

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10511174	0.81[ASN][1000 genomes]
rs13063175	0.81[ASN][1000 genomes]
rs13070584	0.81[ASN][1000 genomes]
rs13084282	0.81[ASN][1000 genomes]
rs13086098	0.91[ASN][1000 genomes]
rs13088964	0.91[ASN][1000 genomes]
rs13098261	0.81[ASN][1000 genomes]
rs16841339	0.81[ASN][1000 genomes]
rs2248792	0.97[EUR][1000 genomes]
rs2342465	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34162135	0.88[ASN][1000 genomes]
rs34468147	0.91[ASN][1000 genomes]
rs34580839	0.95[ASN][1000 genomes]
rs34964323	0.91[ASN][1000 genomes]
rs35217023	0.95[ASN][1000 genomes]
rs35722344	0.91[ASN][1000 genomes]
rs35892771	0.91[ASN][1000 genomes]
rs4928208	0.83[JPT][hapmap]
rs6765840	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs71313550	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs71313551	0.86[ASN][1000 genomes]
rs71313553	0.83[ASN][1000 genomes]
rs71313554	0.86[ASN][1000 genomes]
rs7629812	0.91[ASN][1000 genomes]
rs7649391	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007486	chr3:98597738-99249081	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv530026	chr3:98837320-99340537	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv3916	chr3:99186008-99232052	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	esv1831522	chr3:99207253-99219235	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	esv3422853	chr3:99208019-99342748	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13101237	OR5H6	cis	parietal	SCAN
rs13101237	OR5AC2	cis	cerebellum	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99217000-99219400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr3:99217200-99219400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr3:99217200-99219600	Enhancers	Muscle Satellite Cultured Cells	--
4	chr3:99217200-99219800	Enhancers	NHDF-Ad	bronchial
5	chr3:99217200-99220200	Enhancers	Osteobl	bone
6	chr3:99217400-99219400	Weak transcription	Aorta	Aorta
7	chr3:99217600-99219600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr3:99217600-99219800	Enhancers	HSMM	muscle
9	chr3:99217800-99219600	Enhancers	HUVEC	blood vessel
10	chr3:99217800-99219800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr3:99217800-99219800	Enhancers	NHLF	lung
12	chr3:99217800-99220000	Enhancers	Adipose Nuclei	Adipose
13	chr3:99217800-99220400	Enhancers	Right Atrium	heart
14	chr3:99218200-99219600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr3:99218200-99222200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr3:99218400-99220000	Enhancers	Left Ventricle	heart
17	chr3:99218600-99220200	Enhancers	Right Ventricle	heart
18	chr3:99218800-99219600	Weak transcription	Esophagus	oesophagus
19	chr3:99218800-99219800	Flanking Active TSS	NHEK	skin
20	chr3:99218800-99220000	Enhancers	Ovary	ovary
21	chr3:99218800-99221600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr3:99218800-99224000	Weak transcription	Primary monocytes fromperipheralblood	blood
23	chr3:99218800-99226200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr3:99219000-99219400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr3:99219000-99219400	Weak transcription	HSMMtube	muscle
26	chr3:99219000-99219600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr3:99219000-99219800	Enhancers	Fetal Heart	heart

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