Variant report

Variant	rs3849467
Chromosome Location	chr3:70063781-70063782
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MITF-1	chr3:70062945-70064469	ENSG00000240405
2	lnc-MITF-1	chr3:70062945-70064449	XLOC_002696
3	lnc-MITF-1	chr3:70062852-70064165	NONHSAT090374
4	lnc-MITF-1	chr3:70062945-70064451	NR_110000

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10510994	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11923982	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12495230	0.80[AMR][1000 genomes]
rs12495615	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1491694	0.86[CEU][hapmap];0.91[CHB][hapmap];0.82[AMR][1000 genomes]
rs1491696	0.90[CEU][hapmap];0.90[CHB][hapmap];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1491697	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1491700	0.83[AMR][1000 genomes]
rs17729465	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17729489	0.82[AMR][1000 genomes]
rs17785152	1.00[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17785756	1.00[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];0.82[AMR][1000 genomes]
rs2101636	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs28462307	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2874269	0.83[CHB][hapmap];0.80[ASN][1000 genomes]
rs4293707	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4855334	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4855335	0.82[AMR][1000 genomes]
rs55966844	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs58166970	0.81[ASN][1000 genomes]
rs60251138	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60403843	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60647884	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61645126	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6549264	0.81[AMR][1000 genomes]
rs6549265	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs6549267	0.87[AMR][1000 genomes]
rs6763730	0.84[AMR][1000 genomes]
rs6772684	0.81[AMR][1000 genomes]
rs6799525	1.00[CEU][hapmap];0.86[CHB][hapmap];0.84[AMR][1000 genomes]
rs7431273	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7611660	0.90[CEU][hapmap];0.82[CHB][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7619924	1.00[CEU][hapmap];0.95[CHB][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7632596	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7645353	0.83[AMR][1000 genomes]
rs7649560	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9310181	0.82[AMR][1000 genomes]
rs9815027	1.00[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.84[AMR][1000 genomes]
rs9815287	0.80[AMR][1000 genomes]
rs9818798	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9826811	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9834141	0.81[AMR][1000 genomes]
rs9837453	0.85[AMR][1000 genomes]
rs9840951	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9843867	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9851891	0.80[AMR][1000 genomes]
rs9856462	0.84[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	nsv533396	chr3:69964029-70538306	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	esv3507809	chr3:70058262-70066160	Weak transcription Enhancers Active TSS	Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	esv3507810	chr3:70058712-70066010	Enhancers Weak transcription Active TSS	Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv3507811	chr3:70058712-70066010	Enhancers Weak transcription Active TSS	Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3849467	RP11-460N16.1	cis	Artery Aorta	GTEx

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:70062600-70063800	Enhancers	Aorta	Aorta
2	chr3:70063200-70065800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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