Variant report

Variant	rs2987072
Chromosome Location	chr9:15944448-15944449
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 99 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs1009468	1.00[CHB][hapmap]
rs10283865	0.89[CHB][hapmap];0.85[JPT][hapmap]
rs1080485	0.82[EUR][1000 genomes]
rs10810440	0.88[CHB][hapmap]
rs10810442	1.00[CHB][hapmap]
rs10962147	1.00[CHB][hapmap]
rs10962149	1.00[CHB][hapmap]
rs10962152	1.00[CHB][hapmap]
rs10962153	1.00[CHB][hapmap]
rs10962170	1.00[CHB][hapmap]
rs1169478	0.85[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap]
rs1169479	0.85[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.89[JPT][hapmap];0.91[TSI][hapmap]
rs1169480	0.85[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap]
rs12341679	0.88[CHB][hapmap]
rs1328286	0.85[CEU][hapmap];0.84[TSI][hapmap];0.87[EUR][1000 genomes]
rs1328288	0.86[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1341734	1.00[CHB][hapmap]
rs1355173	1.00[CHB][hapmap]
rs1359953	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1539171	1.00[CHB][hapmap]
rs1572978	1.00[CHB][hapmap]
rs1891211	0.89[CHB][hapmap];0.89[JPT][hapmap]
rs1891212	0.84[CHB][hapmap];0.89[JPT][hapmap]
rs1927696	0.89[CEU][hapmap];0.90[EUR][1000 genomes]
rs1984246	0.89[CHB][hapmap];0.89[JPT][hapmap]
rs2066292	0.94[CHB][hapmap]
rs2096121	1.00[CHB][hapmap]
rs2149231	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2153725	1.00[CHB][hapmap]
rs2153726	1.00[CHB][hapmap]
rs2153727	1.00[CHB][hapmap]
rs2185665	1.00[CHB][hapmap]
rs2225181	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs2382548	0.80[ASN][1000 genomes]
rs2382553	1.00[CHB][hapmap]
rs2794634	1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs2794636	0.84[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs2860316	0.82[ASN][1000 genomes]
rs2891007	1.00[CHB][hapmap]
rs2987008	0.85[EUR][1000 genomes]
rs2987009	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs2987011	0.84[TSI][hapmap]
rs2987012	0.81[CEU][hapmap]
rs2987013	0.89[TSI][hapmap]
rs2987018	0.82[ASN][1000 genomes]
rs2987069	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2987070	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2987071	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3008666	0.81[EUR][1000 genomes]
rs3008672	0.81[EUR][1000 genomes]
rs3008678	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3008681	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs3008686	1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3008749	0.81[CEU][hapmap]
rs3008753	0.82[EUR][1000 genomes]
rs6474966	0.94[CHB][hapmap]
rs7019205	1.00[CHB][hapmap]
rs7019851	1.00[CHB][hapmap]
rs7027202	0.89[CHB][hapmap];0.85[JPT][hapmap]
rs7032457	1.00[CHB][hapmap]
rs7032634	1.00[CHB][hapmap]
rs7034781	0.94[CHB][hapmap]
rs7045018	1.00[CHB][hapmap]
rs7047045	1.00[CHB][hapmap]
rs735962	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs7467156	0.88[CHB][hapmap]
rs7467207	0.83[CHB][hapmap]
rs770191	1.00[CHB][hapmap];0.82[TSI][hapmap]
rs770211	0.80[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs770213	0.81[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs770215	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs7853744	1.00[CHB][hapmap]
rs7861456	0.81[ASN][1000 genomes]
rs7866641	1.00[CHB][hapmap]
rs7869624	1.00[CHB][hapmap]
rs7872912	1.00[CHB][hapmap]
rs9298738	1.00[CHB][hapmap]
rs9298739	1.00[CHB][hapmap]
rs9298740	1.00[CHB][hapmap]
rs9298741	1.00[CHB][hapmap]
rs9406537	1.00[CHB][hapmap]
rs9406542	1.00[CHB][hapmap]
rs9406568	0.82[EUR][1000 genomes]
rs9406569	0.82[ASN][1000 genomes]
rs9407648	1.00[CHB][hapmap]
rs9407649	1.00[CHB][hapmap]
rs9407650	1.00[CHB][hapmap]
rs9407651	1.00[CHB][hapmap]
rs9407652	1.00[CHB][hapmap]
rs9407654	1.00[CHB][hapmap]
rs9407657	1.00[CHB][hapmap]
rs9407661	1.00[CHB][hapmap]
rs9407662	1.00[CHB][hapmap]
rs9650686	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	esv2753625	chr9:15914055-15980320	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer	lncRNA	n/a	inside rSNPs	diseases
3	nsv892637	chr9:15926508-16060746	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv3483970	chr9:15944147-15948125	Weak transcription ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases
5	esv3483971	chr9:15944147-15948125	Weak transcription ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2987072	PLP1	trans	parietal	SCAN
rs2987072	C9orf93	cis	parietal	SCAN
rs2987072	C9orf93	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:15933200-15951400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr9:15936800-15946800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr9:15943800-15954800	Weak transcription	Fetal Lung	lung

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