Variant report

Variant	rs41507950
Chromosome Location	chr2:57953208-57953209
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs12104766	1.00[AMR][1000 genomes]
rs12105180	1.00[AMR][1000 genomes]
rs1520963	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs17039675	1.00[AMR][1000 genomes]
rs17049103	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17049119	1.00[AMR][1000 genomes]
rs17049122	1.00[AMR][1000 genomes]
rs17049169	0.92[YRI][hapmap];1.00[AMR][1000 genomes]
rs17049188	1.00[AMR][1000 genomes]
rs17049192	1.00[AMR][1000 genomes]
rs17049195	1.00[AMR][1000 genomes]
rs17049218	1.00[AMR][1000 genomes]
rs17049234	1.00[AMR][1000 genomes]
rs17049246	1.00[AMR][1000 genomes]
rs17049251	0.90[LWK][hapmap];1.00[AMR][1000 genomes]
rs55811651	1.00[AMR][1000 genomes]
rs56193241	1.00[AMR][1000 genomes]
rs56199322	1.00[AMR][1000 genomes]
rs56393555	1.00[AMR][1000 genomes]
rs58333652	1.00[AMR][1000 genomes]
rs58838819	1.00[AMR][1000 genomes]
rs59146679	1.00[AMR][1000 genomes]
rs59163667	1.00[AMR][1000 genomes]
rs59235511	1.00[AMR][1000 genomes]
rs59691581	1.00[AMR][1000 genomes]
rs60453955	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60462720	1.00[AMR][1000 genomes]
rs60765249	1.00[AMR][1000 genomes]
rs6751864	1.00[AMR][1000 genomes]
rs72939601	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72941503	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72941525	1.00[AMR][1000 genomes]
rs72941526	1.00[AMR][1000 genomes]
rs72941532	1.00[AMR][1000 genomes]
rs72941544	1.00[AMR][1000 genomes]
rs72941589	1.00[AMR][1000 genomes]
rs72943305	1.00[AMR][1000 genomes]
rs72943312	1.00[AMR][1000 genomes]
rs72943328	1.00[AMR][1000 genomes]
rs72943335	1.00[AMR][1000 genomes]
rs72943342	1.00[AMR][1000 genomes]
rs72943350	1.00[AMR][1000 genomes]
rs72943356	1.00[AMR][1000 genomes]
rs72943358	1.00[AMR][1000 genomes]
rs72943369	1.00[AMR][1000 genomes]
rs72943371	1.00[AMR][1000 genomes]
rs73941649	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73942209	1.00[AMR][1000 genomes]
rs73942219	1.00[AMR][1000 genomes]
rs73944124	1.00[AMR][1000 genomes]
rs73944146	1.00[AMR][1000 genomes]
rs7572606	1.00[LWK][hapmap];1.00[AMR][1000 genomes]
rs7600283	1.00[AMR][1000 genomes]
rs952625	1.00[AMR][1000 genomes]
rs952626	1.00[AMR][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:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:57952800-57954000	Enhancers	GM12878-XiMat	blood
2	chr2:57953200-57954200	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr2:57953200-57957600	Weak transcription	Fetal Thymus	thymus

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