Variant report

Variant	rs10962947
Chromosome Location	chr9:17252006-17252007
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 172 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:155)

rs_ID	r²[population]
rs10046851	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10114083	0.82[EUR][1000 genomes]
rs10114688	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10114730	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10116428	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10119297	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10119370	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10120757	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10122987	0.83[EUR][1000 genomes]
rs10123715	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10123745	0.83[EUR][1000 genomes]
rs10124487	0.81[EUR][1000 genomes]
rs10124513	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10125333	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10481559	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10738474	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10738476	0.83[EUR][1000 genomes]
rs10756856	0.81[EUR][1000 genomes]
rs10756858	0.82[AFR][1000 genomes]
rs10756860	0.87[EUR][1000 genomes]
rs10756866	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10756867	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10756869	0.81[EUR][1000 genomes]
rs10756874	0.83[EUR][1000 genomes]
rs10756875	0.83[EUR][1000 genomes]
rs10756876	0.83[EUR][1000 genomes]
rs10756877	0.83[EUR][1000 genomes]
rs10756878	0.82[EUR][1000 genomes]
rs10810739	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10810740	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10810748	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10810749	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10810750	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10810751	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10810752	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10810756	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10810761	0.82[EUR][1000 genomes]
rs10810763	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10810764	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10810765	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10810773	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10810774	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10810775	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10810777	0.83[EUR][1000 genomes]
rs10962950	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10962982	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10962988	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs10963026	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10963042	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10963057	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10963063	0.81[EUR][1000 genomes]
rs12236820	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12337154	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12337171	0.82[EUR][1000 genomes]
rs12342180	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12379102	0.82[EUR][1000 genomes]
rs13290922	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1372702	0.83[EUR][1000 genomes]
rs1576962	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1582030	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1582031	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1583987	0.81[EUR][1000 genomes]
rs1591138	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1759454	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1759613	0.88[EUR][1000 genomes]
rs2044119	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2044120	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2099858	0.83[EUR][1000 genomes]
rs2151290	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2225598	0.83[EUR][1000 genomes]
rs2779773	0.89[EUR][1000 genomes]
rs2779775	0.89[EUR][1000 genomes]
rs2779776	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2780206	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2990670	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3765040	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3808784	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3824391	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3824392	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3861711	0.83[EUR][1000 genomes]
rs4246135	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4246136	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4272484	0.82[EUR][1000 genomes]
rs4409489	0.87[EUR][1000 genomes]
rs4424358	0.86[EUR][1000 genomes]
rs4563978	0.82[EUR][1000 genomes]
rs4961437	0.83[EUR][1000 genomes]
rs4961539	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4961540	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4961541	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4961542	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4961543	0.83[EUR][1000 genomes]
rs4961544	0.82[EUR][1000 genomes]
rs4961545	0.83[EUR][1000 genomes]
rs4961547	0.83[EUR][1000 genomes]
rs4961548	0.83[EUR][1000 genomes]
rs4961552	0.83[EUR][1000 genomes]
rs4961553	0.82[EUR][1000 genomes]
rs593614	0.89[EUR][1000 genomes]
rs595894	0.87[EUR][1000 genomes]
rs605916	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs619380	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs632265	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs645117	0.88[EUR][1000 genomes]
rs6475139	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6475141	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6475142	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6475143	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6475144	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6475145	0.82[EUR][1000 genomes]
rs654521	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs670058	0.89[EUR][1000 genomes]
rs670511	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7018705	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7022024	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7022060	0.81[EUR][1000 genomes]
rs7028593	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7028779	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7028930	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7031133	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7033974	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7037111	0.81[EUR][1000 genomes]
rs7038064	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7038197	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7044462	0.85[ASN][1000 genomes]
rs7044823	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7046933	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7848397	0.82[EUR][1000 genomes]
rs7848980	0.83[EUR][1000 genomes]
rs7849084	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7849085	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7851890	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7854724	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7854802	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7854818	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7858530	0.81[ASN][1000 genomes]
rs7862069	0.83[EUR][1000 genomes]
rs7864270	0.81[EUR][1000 genomes]
rs7864271	0.81[EUR][1000 genomes]
rs7864650	0.83[EUR][1000 genomes]
rs7864919	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7865766	0.81[EUR][1000 genomes]
rs7868700	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7869727	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7870101	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7871926	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7872831	0.82[EUR][1000 genomes]
rs7873708	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7874453	0.81[EUR][1000 genomes]
rs870271	0.89[EUR][1000 genomes]
rs9298772	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9298773	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9298774	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9406666	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9695844	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024799	chr9:16631890-17431827	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	esv2764141	chr9:16903446-17351711	Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv892658	chr9:17041557-17532840	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv892660	chr9:17134245-17269437	Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
5	nsv892661	chr9:17134245-17532840	Flanking Bivalent TSS/Enh Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
6	nsv428537	chr9:17146369-17308494	Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv613693	chr9:17147191-17710407	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
8	nsv471287	chr9:17165698-17708814	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
9	nsv466269	chr9:17165698-17710407	Weak transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
10	nsv892662	chr9:17168867-17329964	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
11	nsv1031269	chr9:17204320-17316969	Flanking Active TSS Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
12	nsv1030291	chr9:17216945-17262803	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
13	nsv466270	chr9:17236376-17377629	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
14	nsv613694	chr9:17236376-17377629	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
15	nsv892663	chr9:17243746-17329964	ZNF genes & repeats Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
16	nsv892664	chr9:17250170-17296630	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS	n/a	n/a	inside rSNPs	diseases
17	nsv892665	chr9:17250170-17371690	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10962947	C9orf39	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:17223600-17279400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr9:17236400-17262000	Weak transcription	Ovary	ovary
3	chr9:17247400-17269000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr9:17249600-17252400	ZNF genes & repeats	Liver	Liver
5	chr9:17249600-17252400	ZNF genes & repeats	Fetal Lung	lung
6	chr9:17249600-17253000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
7	chr9:17249600-17254600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr9:17250800-17252600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr9:17250800-17252600	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
10	chr9:17251000-17252200	ZNF genes & repeats	Fetal Kidney	kidney
11	chr9:17252000-17252600	ZNF genes & repeats	A549	lung
12	chr9:17252000-17255000	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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