Variant report

Variant	rs1809412
Chromosome Location	chr15:79021908-79021909
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:79010677..79012767-chr15:79021718..79023222,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CHRNA5-3	chr15:79021610-79021938	NONHSAT047597

Variant related genes	Relation type
ENSG00000117971	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs11072787	0.89[CEU][hapmap]
rs11072793	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11072794	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11072799	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11629639	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11629824	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11633170	0.94[ASW][hapmap];0.83[MKK][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11633519	0.89[ASN][1000 genomes]
rs11634628	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11852887	0.90[EUR][1000 genomes]
rs11852909	0.94[EUR][1000 genomes]
rs11856441	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12899940	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12901228	0.92[EUR][1000 genomes]
rs12904489	0.82[EUR][1000 genomes]
rs12906977	0.83[EUR][1000 genomes]
rs12907178	0.83[ASN][1000 genomes]
rs12907207	0.84[EUR][1000 genomes]
rs12907432	0.84[EUR][1000 genomes]
rs12907511	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12907536	0.84[EUR][1000 genomes]
rs12913779	0.84[EUR][1000 genomes]
rs1383634	0.93[EUR][1000 genomes]
rs1383635	0.93[EUR][1000 genomes]
rs1809414	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1814880	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1825086	0.93[EUR][1000 genomes]
rs1904920	0.90[EUR][1000 genomes]
rs2017091	0.84[EUR][1000 genomes]
rs2219939	0.93[EUR][1000 genomes]
rs3971868	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4887074	0.84[CEU][hapmap]
rs4887078	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4887085	0.90[ASN][1000 genomes]
rs4887091	0.94[CEU][hapmap]
rs71402966	0.82[EUR][1000 genomes]
rs7176070	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7182567	0.95[CEU][hapmap];0.89[GIH][hapmap];0.85[TSI][hapmap]
rs755998	0.84[EUR][1000 genomes]
rs8030090	0.82[EUR][1000 genomes]
rs8030335	0.82[EUR][1000 genomes]
rs8043123	0.84[CEU][hapmap];0.80[GIH][hapmap]
rs899997	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9888691	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917303	chr15:78491050-79205255	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	122 gene(s)	inside rSNPs	diseases
2	nsv974606	chr15:78996783-79048337	Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv904431	chr15:79006442-79155088	Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1809412	RP11-650L12.2	cis	Muscle Skeletal	GTEx
rs1809412	TMED3	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:79019400-79022000	Enhancers	A549	lung
2	chr15:79020400-79022000	Enhancers	Colon Smooth Muscle	Colon
3	chr15:79020800-79023000	Weak transcription	Fetal Stomach	stomach
4	chr15:79021200-79023400	Weak transcription	Stomach Smooth Muscle	stomach
5	chr15:79021400-79023600	Weak transcription	Rectal Smooth Muscle	rectum

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