Variant report

Variant	rs1955726
Chromosome Location	chr14:39957437-39957438
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CTAGE5-5	chr14:39957187-39959594	NONHSAT036547

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs12050477	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12590172	0.83[CHB][hapmap]
rs12883652	0.80[ASN][1000 genomes]
rs12884747	0.83[ASN][1000 genomes]
rs12886696	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12894855	0.83[CHB][hapmap]
rs12896502	0.83[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs1304254	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17109296	0.94[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17109300	0.83[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs17109328	0.82[ASN][1000 genomes]
rs1807940	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1950330	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1950331	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1950333	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1950334	0.82[ASN][1000 genomes]
rs1950335	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1955729	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2038278	0.80[ASN][1000 genomes]
rs2057137	0.83[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs2057138	0.83[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs2057139	0.81[ASN][1000 genomes]
rs2207293	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2274395	0.83[CHB][hapmap]
rs34687394	0.82[ASN][1000 genomes]
rs35643160	0.83[ASN][1000 genomes]
rs35708308	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35923045	0.82[ASN][1000 genomes]
rs3814860	0.83[CHB][hapmap]
rs4899287	0.82[ASN][1000 genomes]
rs4899291	0.81[ASN][1000 genomes]
rs4902569	0.83[CHB][hapmap]
rs4902570	0.83[CHB][hapmap]
rs4902692	0.83[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs7148377	0.87[CHB][hapmap];0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs7152341	0.82[CHB][hapmap]
rs7158709	0.83[ASN][1000 genomes]
rs7161403	0.83[CHB][hapmap]
rs718364	0.87[CHB][hapmap];0.86[CHD][hapmap];0.92[GIH][hapmap];0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs8006321	0.83[CHB][hapmap]
rs8020250	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	nsv915558	chr14:39944831-40165370	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv456212	chr14:39957437-40096888	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv564418	chr14:39957437-40096888	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:39952400-39958000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr14:39955400-39957800	Weak transcription	Brain Hippocampus Middle	brain
3	chr14:39957200-39959200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr14:39957200-39959600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr14:39957400-39958600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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