Variant report

Variant	rs1507276
Chromosome Location	chr1:86620057-86620058
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ODF2L-3	chr1:86619756-86621905	NONHSAT004264

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs11161752	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11161754	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11161755	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.85[LWK][hapmap];0.80[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11161756	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11161757	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11161758	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11161759	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11578172	0.86[EUR][1000 genomes]
rs11581251	0.82[EUR][1000 genomes]
rs11581326	0.90[EUR][1000 genomes]
rs11583102	0.90[EUR][1000 genomes]
rs11583117	0.90[EUR][1000 genomes]
rs11583120	0.90[EUR][1000 genomes]
rs12068500	0.92[EUR][1000 genomes]
rs12070992	0.88[CHB][hapmap];0.81[JPT][hapmap];0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12072489	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12072806	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12074275	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12076366	1.00[CEU][hapmap];0.88[CHB][hapmap];0.80[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.91[MEX][hapmap];0.87[MKK][hapmap];0.92[TSI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12080986	0.88[CHB][hapmap];0.80[CHD][hapmap];0.84[JPT][hapmap];0.82[MEX][hapmap];0.84[ASN][1000 genomes]
rs1336052	0.87[CEU][hapmap];0.84[EUR][1000 genomes]
rs1336055	0.83[EUR][1000 genomes]
rs1414601	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1507267	0.90[EUR][1000 genomes]
rs1507268	0.82[EUR][1000 genomes]
rs1507282	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1507283	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17128866	0.86[CEU][hapmap];0.86[EUR][1000 genomes]
rs2039601	0.90[EUR][1000 genomes]
rs2174768	0.82[EUR][1000 genomes]
rs2279948	0.82[EUR][1000 genomes]
rs2892908	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.80[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs41287729	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4631724	0.87[CEU][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs59694883	0.83[EUR][1000 genomes]
rs6660694	1.00[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6668627	0.83[EUR][1000 genomes]
rs6676847	0.90[EUR][1000 genomes]
rs6697869	0.90[EUR][1000 genomes]
rs72716183	0.86[EUR][1000 genomes]
rs72716185	0.94[EUR][1000 genomes]
rs72716190	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72716192	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72716194	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72716202	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72718016	0.88[EUR][1000 genomes]
rs72718019	0.86[EUR][1000 genomes]
rs72718023	0.83[EUR][1000 genomes]
rs72718033	0.83[EUR][1000 genomes]
rs72718037	0.82[EUR][1000 genomes]
rs7531445	0.90[EUR][1000 genomes]
rs7536402	0.90[EUR][1000 genomes]
rs954354	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817212	chr1:86127851-86658426	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv546722	chr1:86278315-86891073	Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1010312	chr1:86469730-86686426	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1012467	chr1:86494935-86686426	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv1009092	chr1:86532988-86724805	Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Active TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv535024	chr1:86532988-86724805	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv830481	chr1:86550274-86737290	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	esv2763578	chr1:86584695-86622285	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv1003838	chr1:86591841-87212231	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86617400-86620600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr1:86617800-86621600	Weak transcription	HSMM	muscle
3	chr1:86618000-86620200	Weak transcription	NHDF-Ad	bronchial
4	chr1:86618200-86620400	Enhancers	Colon Smooth Muscle	Colon
5	chr1:86618600-86620400	Enhancers	Fetal Lung	lung
6	chr1:86619200-86620400	Weak transcription	NHLF	lung
7	chr1:86619600-86620600	Enhancers	Osteobl	bone
8	chr1:86619800-86620400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr1:86619800-86622400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr1:86620000-86620200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr1:86620000-86620200	Flanking Active TSS	Rectal Smooth Muscle	rectum
12	chr1:86620000-86620200	Enhancers	Stomach Smooth Muscle	stomach
13	chr1:86620000-86620200	Enhancers	NHEK	skin
14	chr1:86620000-86620400	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr1:86620000-86620400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr1:86620000-86620400	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr1:86620000-86620400	Enhancers	Fetal Stomach	stomach
18	chr1:86620000-86620800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr1:86620000-86620800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr1:86620000-86620800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr1:86620000-86620800	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr1:86620000-86621000	Enhancers	NH-A	brain
23	chr1:86620000-86623000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin

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