Variant report

Variant	rs1328286
Chromosome Location	chr9:15918933-15918934
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 130 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:128)

rs_ID	r²[population]
rs10733305	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs10738417	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs10738419	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs10738420	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs10756697	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs10756704	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs10756709	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs10756710	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs10756711	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs10756714	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs10756715	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs10756720	0.90[CHB][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs10756721	0.81[ASN][1000 genomes]
rs10756722	0.85[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs10756726	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs10756728	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs10756729	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs1080485	0.81[ASN][1000 genomes]
rs10810439	1.00[CHB][hapmap];0.85[CHD][hapmap]
rs10810446	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs10810455	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs10810461	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs10810462	0.90[CHB][hapmap]
rs10810479	0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs10810480	0.81[ASN][1000 genomes]
rs10810481	0.81[ASN][1000 genomes]
rs10810482	0.81[ASN][1000 genomes]
rs10810483	0.85[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs10810484	0.85[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs10810485	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs10810486	0.90[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs10810487	0.90[CHB][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs10810488	0.90[CHB][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs10810501	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs10810502	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs10810506	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs10810509	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs10962142	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs10962151	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs10962156	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs10962157	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs10962158	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs10962225	0.85[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs10962227	0.90[CHB][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs1169478	0.85[CEU][hapmap]
rs1169479	0.85[CEU][hapmap];0.91[TSI][hapmap]
rs1169480	0.85[CEU][hapmap]
rs12378499	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs12379234	0.84[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs1328283	0.85[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs1328288	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13287834	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs13292699	0.81[ASN][1000 genomes]
rs13296360	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs13297383	0.84[ASN][1000 genomes]
rs1341732	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs1341737	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs1341738	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs1359952	0.95[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.80[TSI][hapmap];0.98[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1359953	0.89[CEU][hapmap];0.95[EUR][1000 genomes]
rs1410444	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs1410445	0.87[ASN][1000 genomes]
rs1410446	0.82[ASN][1000 genomes]
rs1539172	1.00[CHB][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap]
rs1539173	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs1592099	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs1927696	0.89[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1927697	0.82[ASN][1000 genomes]
rs1927698	0.85[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs2105315	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs2182936	0.91[ASN][1000 genomes]
rs2185663	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs2225181	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2225182	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs2382540	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs2382554	0.80[ASN][1000 genomes]
rs2794634	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs2794636	0.88[CEU][hapmap]
rs2987009	0.85[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.80[EUR][1000 genomes]
rs2987010	0.90[CHB][hapmap];0.90[JPT][hapmap];0.89[TSI][hapmap]
rs2987011	0.95[CHB][hapmap];0.90[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.96[TSI][hapmap]
rs2987012	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs2987013	0.95[CHB][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.83[LWK][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap]
rs2987014	0.94[CHB][hapmap];0.90[JPT][hapmap]
rs2987069	0.89[CEU][hapmap];0.88[EUR][1000 genomes]
rs2987070	0.93[CEU][hapmap];0.89[EUR][1000 genomes]
rs2987071	0.85[CEU][hapmap];0.89[EUR][1000 genomes]
rs2987072	0.85[CEU][hapmap];0.84[TSI][hapmap];0.87[EUR][1000 genomes]
rs3008666	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs3008672	0.81[ASN][1000 genomes]
rs3008678	0.87[EUR][1000 genomes]
rs3008681	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3008683	0.82[YRI][hapmap]
rs3008686	0.93[CEU][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3008747	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs3008748	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs3008749	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs3008751	0.85[CHB][hapmap]
rs3008753	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs4146290	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs4146291	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs4146293	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs4472620	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs4582646	0.85[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs4740624	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs4740628	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs4741535	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs4741545	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs4741546	1.00[CHB][hapmap];0.82[CHD][hapmap];0.82[JPT][hapmap]
rs4741548	0.86[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs4741552	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs4741553	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs4961713	0.81[ASN][1000 genomes]
rs6474967	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs6474974	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs7043770	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs735962	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.90[AFR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7469281	0.83[YRI][hapmap]
rs770191	0.82[JPT][hapmap];0.85[TSI][hapmap]
rs770211	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs770213	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs7849380	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs7860528	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs7860755	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs7873776	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs950234	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs955369	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs961117	0.85[CHB][hapmap];0.86[JPT][hapmap];0.81[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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1328286	C9orf93	cis	cerebellum	SCAN
rs1328286	C9orf93	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:15915800-15920800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr9:15916000-15920600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr9:15918200-15930800	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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