Variant report

Variant	rs12236820
Chromosome Location	chr9:17249540-17249541
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 154 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:139)

rs_ID	r²[population]
rs10046851	0.82[EUR][1000 genomes]
rs10114083	0.80[EUR][1000 genomes]
rs10114688	0.82[EUR][1000 genomes]
rs10114730	0.82[EUR][1000 genomes]
rs10116428	0.82[EUR][1000 genomes]
rs10119297	0.82[EUR][1000 genomes]
rs10119370	0.82[EUR][1000 genomes]
rs10120757	0.82[EUR][1000 genomes]
rs10122987	0.81[EUR][1000 genomes]
rs10123715	0.82[EUR][1000 genomes]
rs10123745	0.81[EUR][1000 genomes]
rs10124513	0.82[EUR][1000 genomes]
rs10125333	0.83[EUR][1000 genomes]
rs10481559	0.82[EUR][1000 genomes]
rs10738474	0.82[EUR][1000 genomes]
rs10738476	0.81[EUR][1000 genomes]
rs10756860	0.85[EUR][1000 genomes]
rs10756866	0.82[EUR][1000 genomes]
rs10756867	0.82[EUR][1000 genomes]
rs10756874	0.81[EUR][1000 genomes]
rs10756875	0.81[EUR][1000 genomes]
rs10756876	0.81[EUR][1000 genomes]
rs10756877	0.81[EUR][1000 genomes]
rs10756878	0.80[EUR][1000 genomes]
rs10810739	0.86[EUR][1000 genomes]
rs10810740	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10810748	0.86[EUR][1000 genomes]
rs10810749	0.86[EUR][1000 genomes]
rs10810750	0.85[EUR][1000 genomes]
rs10810751	0.86[EUR][1000 genomes]
rs10810752	0.86[EUR][1000 genomes]
rs10810756	0.82[EUR][1000 genomes]
rs10810761	0.81[EUR][1000 genomes]
rs10810763	0.83[EUR][1000 genomes]
rs10810764	0.83[EUR][1000 genomes]
rs10810765	0.82[EUR][1000 genomes]
rs10810773	0.81[EUR][1000 genomes]
rs10810774	0.81[EUR][1000 genomes]
rs10810775	0.81[EUR][1000 genomes]
rs10810777	0.81[EUR][1000 genomes]
rs10962947	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10962950	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10962982	0.87[EUR][1000 genomes]
rs10963026	0.86[EUR][1000 genomes]
rs10963042	0.82[EUR][1000 genomes]
rs10963057	0.81[EUR][1000 genomes]
rs12337154	0.82[EUR][1000 genomes]
rs12337171	0.81[EUR][1000 genomes]
rs12342180	0.82[EUR][1000 genomes]
rs12379102	0.80[EUR][1000 genomes]
rs13290922	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1372702	0.81[EUR][1000 genomes]
rs1576962	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1582030	0.81[EUR][1000 genomes]
rs1582031	0.81[EUR][1000 genomes]
rs1759454	0.87[EUR][1000 genomes]
rs1759613	0.85[EUR][1000 genomes]
rs2044119	0.81[EUR][1000 genomes]
rs2044120	0.81[EUR][1000 genomes]
rs2099858	0.81[EUR][1000 genomes]
rs2151290	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2225598	0.81[EUR][1000 genomes]
rs2779773	0.87[EUR][1000 genomes]
rs2779775	0.87[EUR][1000 genomes]
rs2779776	0.85[EUR][1000 genomes]
rs2780206	0.83[EUR][1000 genomes]
rs2990670	0.88[EUR][1000 genomes]
rs3765040	0.83[EUR][1000 genomes]
rs3808784	0.83[EUR][1000 genomes]
rs3824391	0.82[EUR][1000 genomes]
rs3824392	0.82[EUR][1000 genomes]
rs3861711	0.81[EUR][1000 genomes]
rs4246135	0.83[EUR][1000 genomes]
rs4246136	0.82[EUR][1000 genomes]
rs4272484	0.81[EUR][1000 genomes]
rs4409489	0.85[EUR][1000 genomes]
rs4424358	0.84[EUR][1000 genomes]
rs4563978	0.81[EUR][1000 genomes]
rs4961437	0.81[EUR][1000 genomes]
rs4961539	0.83[EUR][1000 genomes]
rs4961540	0.82[EUR][1000 genomes]
rs4961541	0.81[EUR][1000 genomes]
rs4961542	0.81[EUR][1000 genomes]
rs4961543	0.81[EUR][1000 genomes]
rs4961544	0.81[EUR][1000 genomes]
rs4961545	0.81[EUR][1000 genomes]
rs4961547	0.81[EUR][1000 genomes]
rs4961548	0.82[EUR][1000 genomes]
rs4961552	0.81[EUR][1000 genomes]
rs4961553	0.81[EUR][1000 genomes]
rs593614	0.86[EUR][1000 genomes]
rs595894	0.86[EUR][1000 genomes]
rs605916	0.88[EUR][1000 genomes]
rs619380	0.87[EUR][1000 genomes]
rs632265	0.87[EUR][1000 genomes]
rs645117	0.86[EUR][1000 genomes]
rs6475139	0.81[EUR][1000 genomes]
rs6475141	0.82[EUR][1000 genomes]
rs6475142	0.81[EUR][1000 genomes]
rs6475143	0.82[EUR][1000 genomes]
rs6475144	0.82[EUR][1000 genomes]
rs6475145	0.81[EUR][1000 genomes]
rs654521	0.90[EUR][1000 genomes]
rs670058	0.86[EUR][1000 genomes]
rs670511	0.88[EUR][1000 genomes]
rs7018705	0.84[EUR][1000 genomes]
rs7022024	0.83[EUR][1000 genomes]
rs7028593	0.83[EUR][1000 genomes]
rs7028779	0.82[EUR][1000 genomes]
rs7028930	0.83[EUR][1000 genomes]
rs7031133	0.83[EUR][1000 genomes]
rs7033974	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7038064	0.82[EUR][1000 genomes]
rs7038197	0.83[EUR][1000 genomes]
rs7044823	0.83[EUR][1000 genomes]
rs7046933	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7848397	0.80[EUR][1000 genomes]
rs7848980	0.81[EUR][1000 genomes]
rs7849084	0.86[EUR][1000 genomes]
rs7849085	0.86[EUR][1000 genomes]
rs7851890	0.81[EUR][1000 genomes]
rs7854724	0.81[EUR][1000 genomes]
rs7854802	0.82[EUR][1000 genomes]
rs7854818	0.81[EUR][1000 genomes]
rs7862069	0.81[EUR][1000 genomes]
rs7864650	0.81[EUR][1000 genomes]
rs7864919	0.81[EUR][1000 genomes]
rs7868700	0.81[EUR][1000 genomes]
rs7869727	0.81[EUR][1000 genomes]
rs7870101	0.82[EUR][1000 genomes]
rs7871926	0.80[EUR][1000 genomes]
rs7872831	0.81[EUR][1000 genomes]
rs7873708	0.80[EUR][1000 genomes]
rs870271	0.87[EUR][1000 genomes]
rs9298772	0.83[EUR][1000 genomes]
rs9298773	0.81[EUR][1000 genomes]
rs9298774	0.83[EUR][1000 genomes]
rs9406666	0.87[EUR][1000 genomes]
rs9695844	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12236820	C9orf39	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:16 , 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	chr9:17229800-17251600	Weak transcription	HSMM	muscle
3	chr9:17235000-17249600	Weak transcription	Dnd41	blood
4	chr9:17236400-17262000	Weak transcription	Ovary	ovary
5	chr9:17241000-17249800	Weak transcription	Fetal Heart	heart
6	chr9:17244600-17249600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr9:17247200-17251000	Weak transcription	Fetal Kidney	kidney
8	chr9:17247400-17249600	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr9:17247400-17249600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr9:17247400-17269000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr9:17248000-17249600	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr9:17248000-17250800	Weak transcription	Left Ventricle	heart
13	chr9:17248200-17249600	Weak transcription	Liver	Liver
14	chr9:17248400-17249600	Weak transcription	Fetal Lung	lung
15	chr9:17249400-17249600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr9:17249400-17249800	ZNF genes & repeats	Right Ventricle	heart

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