Variant report

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-VRK2-2	chr2:57952830-57953284	XLOC_001484

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10186791	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10195687	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10196378	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10204616	0.86[EUR][1000 genomes]
rs1040224	0.82[CEU][hapmap]
rs1040225	0.82[CEU][hapmap]
rs10496076	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13402331	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13418015	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2465804	0.82[CEU][hapmap]
rs2678901	0.82[CEU][hapmap]
rs2678903	0.82[CEU][hapmap]
rs2678905	0.82[CEU][hapmap]
rs2678906	0.82[CEU][hapmap]
rs2678908	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.82[TSI][hapmap]
rs2717001	0.82[CEU][hapmap];0.80[CHD][hapmap];1.00[GIH][hapmap];0.82[TSI][hapmap]
rs2717002	0.82[CEU][hapmap];0.81[CHD][hapmap];0.98[GIH][hapmap];0.82[TSI][hapmap]
rs2717004	0.82[CEU][hapmap]
rs2717006	0.89[CEU][hapmap]
rs3886275	0.89[EUR][1000 genomes]
rs6720888	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007118	chr2:57562051-58147588	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv874193	chr2:57758608-58066673	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1006688	chr2:57822953-58030203	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv874196	chr2:57946148-58220320	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 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	chr2:57952400-57953000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr2:57952400-57953000	Enhancers	Brain Germinal Matrix	brain
3	chr2:57952400-57953200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr2:57952400-57953200	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr2:57952600-57953200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:57952600-57953200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr2:57952600-57953200	Strong transcription	Fetal Thymus	thymus
8	chr2:57952800-57954000	Enhancers	GM12878-XiMat	blood

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