Variant report

Variant	rs7040549
Chromosome Location	chr9:15890291-15890292
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SNAPC3-1	chr9:15888981-15890761	NONHSAT130281

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10962193	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10962194	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11999303	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12005062	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12005485	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12005521	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12683523	0.80[ASN][1000 genomes]
rs12683980	0.93[AMR][1000 genomes]
rs12684785	0.93[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12684808	0.92[ASN][1000 genomes]
rs12685476	0.93[AMR][1000 genomes]
rs12685963	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12686591	0.93[AMR][1000 genomes]
rs1328266	0.93[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1328267	0.93[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1328268	0.93[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1396705	1.00[EUR][1000 genomes]
rs1536685	0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1536686	0.80[ASN][1000 genomes]
rs16933504	1.00[EUR][1000 genomes]
rs16933544	1.00[EUR][1000 genomes]
rs16933805	0.95[ASN][1000 genomes]
rs16933814	0.93[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2987062	0.80[ASN][1000 genomes]
rs3008684	0.80[ASN][1000 genomes]
rs3008685	0.80[ASN][1000 genomes]
rs34816651	1.00[EUR][1000 genomes]
rs57592105	0.83[ASN][1000 genomes]
rs59779354	0.80[ASN][1000 genomes]
rs59923163	0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs60354508	0.87[AMR][1000 genomes]
rs60572069	1.00[EUR][1000 genomes]
rs6474968	1.00[EUR][1000 genomes]
rs7026090	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7029375	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7029410	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7032595	1.00[EUR][1000 genomes]
rs7035048	1.00[EUR][1000 genomes]
rs7040071	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7040580	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7040928	0.93[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7044984	0.93[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs73411567	0.87[AMR][1000 genomes]
rs73411570	0.87[AMR][1000 genomes]
rs73411572	0.87[AMR][1000 genomes]
rs73416209	1.00[EUR][1000 genomes]
rs73416213	1.00[EUR][1000 genomes]
rs73416233	1.00[EUR][1000 genomes]
rs73416254	1.00[EUR][1000 genomes]
rs73416261	1.00[EUR][1000 genomes]
rs73416285	1.00[EUR][1000 genomes]
rs73422714	0.83[ASN][1000 genomes]
rs73422737	0.80[ASN][1000 genomes]
rs770207	0.82[ASN][1000 genomes]
rs770219	0.80[ASN][1000 genomes]
rs7847946	1.00[EUR][1000 genomes]
rs7856304	0.80[ASN][1000 genomes]
rs7861533	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7866472	0.93[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7866699	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7867018	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7867521	0.80[ASN][1000 genomes]
rs7869609	1.00[EUR][1000 genomes]
rs7870166	1.00[EUR][1000 genomes]
rs7870244	1.00[EUR][1000 genomes]
rs809493	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv892625	chr9:15326251-16064850	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv892627	chr9:15397969-15909450	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:15877000-15903400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr9:15884200-15891800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr9:15884200-15892200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr9:15885800-15892200	Weak transcription	Primary hematopoietic stem cells	blood
5	chr9:15889000-15890800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr9:15889000-15892800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr9:15889400-15890400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr9:15889800-15890400	Enhancers	Osteobl	bone
9	chr9:15889800-15891800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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