Variant report

Variant	rs10962961
Chromosome Location	chr9:17262502-17262503
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 121 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10114324	0.83[AFR][1000 genomes]
rs10756863	0.85[AFR][1000 genomes]
rs10756865	0.83[AFR][1000 genomes]
rs10810788	0.81[EUR][1000 genomes]
rs10962917	0.89[EUR][1000 genomes]
rs10962922	0.84[AFR][1000 genomes]
rs10962924	0.84[AFR][1000 genomes]
rs10962925	0.86[AFR][1000 genomes]
rs10962933	0.80[AFR][1000 genomes]
rs10962938	0.80[AFR][1000 genomes]
rs10962942	0.80[AFR][1000 genomes]
rs10962960	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10962962	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10962963	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10962964	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10962965	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10962966	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10962985	0.81[AFR][1000 genomes]
rs10962987	0.84[AFR][1000 genomes]
rs10962989	0.83[AFR][1000 genomes]
rs10963011	0.80[AFR][1000 genomes]
rs10963012	0.83[AFR][1000 genomes]
rs1113382	0.83[AFR][1000 genomes]
rs11531707	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11534160	0.80[AFR][1000 genomes]
rs11536700	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11543981	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11543983	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11562139	0.81[AMR][1000 genomes]
rs11562140	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12000610	0.84[AMR][1000 genomes]
rs12235987	0.80[AFR][1000 genomes]
rs13288412	0.84[AMR][1000 genomes]
rs13289731	0.84[AMR][1000 genomes]
rs1576959	0.80[AFR][1000 genomes]
rs1576960	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1759452	0.86[AFR][1000 genomes]
rs1759453	0.87[AFR][1000 genomes]
rs1759459	0.86[AFR][1000 genomes]
rs1759460	0.86[AFR][1000 genomes]
rs1759461	0.86[AFR][1000 genomes]
rs1759462	0.86[AFR][1000 genomes]
rs1759616	0.86[AFR][1000 genomes]
rs1759617	0.85[AFR][1000 genomes]
rs1759619	0.86[AFR][1000 genomes]
rs1930643	0.85[AFR][1000 genomes]
rs1930646	0.82[AFR][1000 genomes]
rs2095145	0.83[AFR][1000 genomes]
rs2383010	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2780204	0.86[AFR][1000 genomes]
rs2780205	0.87[AFR][1000 genomes]
rs2780207	0.87[AFR][1000 genomes]
rs2891110	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3808785	0.86[AFR][1000 genomes]
rs3814137	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs3814138	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs3814139	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs4147023	0.80[AFR][1000 genomes]
rs4272490	0.90[EUR][1000 genomes]
rs4430173	0.80[AFR][1000 genomes]
rs4458955	0.92[EUR][1000 genomes]
rs55829722	0.81[AFR][1000 genomes]
rs56402716	0.81[AMR][1000 genomes]
rs57290709	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57750931	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs585682	0.87[AFR][1000 genomes]
rs599626	0.86[AFR][1000 genomes]
rs600041	0.87[AFR][1000 genomes]
rs600133	0.87[AFR][1000 genomes]
rs60691286	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs614412	0.87[AFR][1000 genomes]
rs614471	0.87[AFR][1000 genomes]
rs619357	0.87[AFR][1000 genomes]
rs631300	0.87[AFR][1000 genomes]
rs632176	0.87[AFR][1000 genomes]
rs632255	0.81[AFR][1000 genomes]
rs632313	0.86[AFR][1000 genomes]
rs634383	0.87[AFR][1000 genomes]
rs634446	0.87[AFR][1000 genomes]
rs643776	0.86[AFR][1000 genomes]
rs647013	0.86[AFR][1000 genomes]
rs6475121	0.94[EUR][1000 genomes]
rs6475125	0.80[AFR][1000 genomes]
rs6475127	0.85[AFR][1000 genomes]
rs6475128	0.82[AFR][1000 genomes]
rs6475129	0.83[AFR][1000 genomes]
rs677490	0.87[AFR][1000 genomes]
rs679666	0.86[AFR][1000 genomes]
rs7020918	0.84[AMR][1000 genomes]
rs7027051	0.87[AFR][1000 genomes]
rs7034768	0.80[AFR][1000 genomes]
rs7035318	0.80[AFR][1000 genomes]
rs7035525	0.80[AFR][1000 genomes]
rs7037408	0.84[AMR][1000 genomes]
rs7040666	0.81[AMR][1000 genomes]
rs7043703	0.80[AFR][1000 genomes]
rs7044254	0.80[AFR][1000 genomes]
rs7874597	0.85[AFR][1000 genomes]
rs9407792	0.83[AFR][1000 genomes]
rs9407804	0.87[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 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
18	nsv892666	chr9:17256043-17280616	Active TSS ZNF genes & repeats Enhancers Strong transcription Weak transcription Flanking Active TSS	n/a	n/a	inside rSNPs	diseases
19	esv3340155	chr9:17260152-17264350	ZNF genes & repeats Weak transcription Active TSS	n/a	n/a	inside rSNPs	diseases
20	esv13106	chr9:17260551-17262869	ZNF genes & repeats Active TSS Weak transcription	n/a	n/a	inside rSNPs	diseases
21	esv3422736	chr9:17261352-17265550	ZNF genes & repeats Weak transcription Active TSS	n/a	n/a	inside rSNPs	diseases

No data

Chromatin state (count:14 , 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	chr9:17247400-17269000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr9:17259200-17262800	Weak transcription	Fetal Brain Male	brain
4	chr9:17260600-17269000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr9:17261600-17262800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr9:17261600-17262800	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr9:17261800-17262600	ZNF genes & repeats	Liver	Liver
8	chr9:17261800-17262800	ZNF genes & repeats	Adipose Nuclei	Adipose
9	chr9:17262000-17262800	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
10	chr9:17262000-17262800	ZNF genes & repeats	Fetal Lung	lung
11	chr9:17262000-17262800	ZNF genes & repeats	Ovary	ovary
12	chr9:17262400-17262800	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr9:17262400-17262800	ZNF genes & repeats	Left Ventricle	heart
14	chr9:17262400-17263000	ZNF genes & repeats	Dnd41	blood

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