Variant report

Variant	rs4902692
Chromosome Location	chr14:39939758-39939759
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CTAGE5-1	chr14:39939522-39939958	XLOC_010811
2	lnc-CTAGE5-1	chr14:39939522-39939938	XLOC_010811
3	lnc-CTAGE5-1	chr14:39939522-39939938	XLOC_010811
4	lnc-CTAGE5-1	chr14:39939522-39939944	NONHSAT036535

Extended variants
information (count: 87 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10137905	0.82[CHB][hapmap]
rs11157067	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11847057	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12587625	0.95[AFR][1000 genomes]
rs12588110	0.95[AFR][1000 genomes]
rs12588175	0.93[AFR][1000 genomes]
rs12588483	0.96[AFR][1000 genomes]
rs12589427	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12590172	0.82[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs12880644	0.95[AFR][1000 genomes]
rs12884747	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12886696	0.81[ASN][1000 genomes]
rs12886769	0.89[AFR][1000 genomes]
rs12894147	0.97[ASN][1000 genomes]
rs12894855	0.83[CHB][hapmap]
rs12896502	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1304254	0.83[ASN][1000 genomes]
rs17109296	0.83[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs17109300	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17109328	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1807940	0.81[ASN][1000 genomes]
rs1950329	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1950330	0.82[ASN][1000 genomes]
rs1950331	0.81[ASN][1000 genomes]
rs1950333	0.81[ASN][1000 genomes]
rs1950334	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1950335	0.81[ASN][1000 genomes]
rs1950336	0.98[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs1950338	0.97[AFR][1000 genomes]
rs1955718	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1955726	0.81[ASN][1000 genomes]
rs1955729	0.84[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs2057137	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2057138	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2057139	0.94[ASN][1000 genomes]
rs2207291	0.97[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2207293	0.81[ASN][1000 genomes]
rs2274395	0.82[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs2274396	0.82[CHB][hapmap]
rs2415549	0.95[AFR][1000 genomes]
rs2415550	0.98[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2899889	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34432449	0.96[ASN][1000 genomes]
rs34649642	0.96[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs34687394	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35459433	0.95[AFR][1000 genomes]
rs35553183	0.95[AFR][1000 genomes]
rs35643160	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35693868	0.93[AFR][1000 genomes]
rs35708308	0.83[ASN][1000 genomes]
rs35923045	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs36010374	0.98[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs3814860	0.82[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs4899277	0.95[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs4899278	0.99[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs4899287	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4899291	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4902569	0.82[CHB][hapmap]
rs4902570	0.82[CHB][hapmap]
rs4902622	0.91[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs4902636	0.96[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs4902637	0.96[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs4902648	0.87[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs4902665	0.95[AFR][1000 genomes]
rs4902676	0.97[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs56046902	0.95[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs71407788	0.85[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs71407789	0.97[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs7140983	0.89[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs7152341	0.82[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs7152935	0.97[AFR][1000 genomes]
rs7158709	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7161403	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs719455	0.92[CHB][hapmap];0.83[JPT][hapmap]
rs72675487	0.95[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs8003397	0.96[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs8003621	0.92[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs8006123	0.95[AFR][1000 genomes]
rs8006321	0.82[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs8020250	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs910370	0.92[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs910371	0.97[AFR][1000 genomes];0.83[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	nsv1037183	chr14:39736939-39949233	Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv542048	chr14:39736939-39949233	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	esv3523177	chr14:39875036-40128325	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	esv3523178	chr14:39875036-40128325	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
5	nsv832774	chr14:39897746-40060823	Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:39938600-39943000	Weak transcription	Left Ventricle	heart
2	chr14:39938800-39943400	Weak transcription	GM12878-XiMat	blood
3	chr14:39938800-39943400	Weak transcription	HepG2	liver
4	chr14:39939000-39942000	Weak transcription	Brain Angular Gyrus	brain
5	chr14:39939000-39942200	Weak transcription	Brain Anterior Caudate	brain
6	chr14:39939000-39943000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr14:39939000-39946000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr14:39939000-39954600	Weak transcription	Brain Hippocampus Middle	brain

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