Variant report

Variant	rs2987079
Chromosome Location	chr9:16010931-16010932
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 169 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:165)

rs_ID	r²[population]
rs10733305	0.90[CHB][hapmap]
rs10738417	0.80[CHB][hapmap];0.86[JPT][hapmap]
rs10738419	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs10738420	0.90[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs10738422	0.89[ASN][1000 genomes]
rs10756709	0.90[CHB][hapmap]
rs10756710	0.90[CHB][hapmap]
rs10756711	0.90[CHB][hapmap]
rs10756714	0.80[CHB][hapmap];0.81[JPT][hapmap]
rs10756715	0.86[JPT][hapmap]
rs10756720	0.80[CHB][hapmap];0.86[JPT][hapmap]
rs10756722	0.86[JPT][hapmap]
rs10756724	0.82[JPT][hapmap]
rs10756726	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs10756728	0.86[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs10756729	0.86[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs10756730	0.82[ASN][1000 genomes]
rs10756731	0.82[ASN][1000 genomes]
rs10756733	0.83[ASN][1000 genomes]
rs1080485	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10810455	0.90[CHB][hapmap];0.80[JPT][hapmap]
rs10810461	0.80[CHB][hapmap];0.86[JPT][hapmap]
rs10810479	0.81[JPT][hapmap]
rs10810483	0.86[JPT][hapmap]
rs10810484	0.86[JPT][hapmap]
rs10810485	0.86[JPT][hapmap]
rs10810486	0.91[JPT][hapmap]
rs10810487	0.80[CHB][hapmap];0.91[JPT][hapmap]
rs10810488	0.80[CHB][hapmap];0.91[JPT][hapmap]
rs10810501	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs10810502	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs10810506	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs10810509	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs10810514	0.89[ASN][1000 genomes]
rs10962225	0.86[JPT][hapmap]
rs10962227	0.80[CHB][hapmap];0.91[JPT][hapmap]
rs10962244	0.83[ASN][1000 genomes]
rs10962256	0.83[ASN][1000 genomes]
rs1169478	0.89[CEU][hapmap]
rs1169479	0.88[CEU][hapmap];0.91[TSI][hapmap]
rs1169480	0.88[CEU][hapmap]
rs12379234	0.86[JPT][hapmap]
rs1328265	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1328269	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1328271	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1328283	0.86[JPT][hapmap]
rs1328286	0.81[CEU][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];0.93[TSI][hapmap]
rs1328288	0.82[CEU][hapmap]
rs1341732	0.84[CHB][hapmap];0.84[JPT][hapmap]
rs1359950	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1359951	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1359952	0.85[CHB][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap]
rs1359953	0.85[CEU][hapmap]
rs1410444	0.91[JPT][hapmap]
rs1576171	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1887664	0.89[ASN][1000 genomes]
rs1927696	0.90[JPT][hapmap]
rs1927698	0.86[JPT][hapmap]
rs1927699	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1927700	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1927701	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1927702	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2017943	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2094522	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2149231	0.89[EUR][1000 genomes]
rs2225181	0.81[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap]
rs2225182	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs2382543	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2382544	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2382545	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2382546	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2382547	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2382548	0.94[EUR][1000 genomes]
rs2794634	0.89[CEU][hapmap]
rs2794636	0.92[CEU][hapmap]
rs2860316	0.97[EUR][1000 genomes]
rs2891003	0.82[ASN][1000 genomes]
rs2987008	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2987009	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2987010	0.89[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2987011	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2987012	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2987013	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2987014	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2987016	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2987017	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2987018	0.97[EUR][1000 genomes]
rs2987019	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2987020	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2987021	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2987022	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2987023	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2987024	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2987025	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2987039	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2987041	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2987042	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2987069	0.85[CEU][hapmap]
rs2987070	0.89[CEU][hapmap]
rs2987071	0.96[CEU][hapmap]
rs2987072	0.89[CEU][hapmap];0.91[TSI][hapmap]
rs2987081	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2987086	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2987090	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2987096	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2987098	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2987099	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3008666	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3008672	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3008681	0.85[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap]
rs3008686	0.89[CEU][hapmap]
rs3008710	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3008714	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3008715	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3008717	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3008719	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3008723	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3008726	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3008727	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3008728	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3008729	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3008730	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3008732	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3008736	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3008738	0.80[ASN][1000 genomes]
rs3008739	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3008742	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3008744	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3008745	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3008747	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3008748	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3008749	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3008753	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3118736	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3824502	0.83[ASN][1000 genomes]
rs4146293	0.90[CHB][hapmap]
rs4442245	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4472620	0.86[JPT][hapmap]
rs4475627	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4582646	0.86[JPT][hapmap]
rs4740628	0.80[CHB][hapmap];0.86[JPT][hapmap]
rs4740629	0.83[ASN][1000 genomes]
rs4741545	0.90[CHB][hapmap]
rs4741546	0.90[CHB][hapmap];0.82[CHD][hapmap]
rs4741548	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs4741552	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs4741553	0.86[CHB][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs6474987	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6474988	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6474989	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7023326	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs723756	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs735962	0.85[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap]
rs770191	0.83[TSI][hapmap]
rs770211	0.92[CEU][hapmap]
rs770213	0.92[CEU][hapmap]
rs770215	0.81[CEU][hapmap]
rs7849380	0.90[CHB][hapmap];0.80[JPT][hapmap]
rs9406568	0.83[EUR][1000 genomes]
rs9406569	0.83[EUR][1000 genomes]
rs9406581	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9407697	0.86[EUR][1000 genomes]
rs9407702	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs961117	0.86[JPT][hapmap]
rs9969791	0.80[CHB][hapmap]

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	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	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
3	nsv949463	chr9:15970668-16377360	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv831521	chr9:15974174-16106565	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2987079	C9orf93	cis	cerebellum	SCAN
rs2987079	C9orf93	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:16001600-16011800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr9:16002400-16012800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr9:16010400-16011000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr9:16010400-16011000	Enhancers	NH-A	brain
5	chr9:16010400-16013400	Enhancers	Osteobl	bone
6	chr9:16010600-16011800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr9:16010600-16011800	Weak transcription	NHDF-Ad	bronchial

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