Variant report

Variant	rs12489298
Chromosome Location	chr3:86865089-86865090
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 146 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:131)

rs_ID	r²[population]
rs10470570	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11127959	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11127961	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs11127962	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs11714652	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11718876	0.90[EUR][1000 genomes]
rs11718877	0.90[EUR][1000 genomes]
rs11718975	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11917335	0.81[EUR][1000 genomes]
rs12485477	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs12487818	0.91[EUR][1000 genomes]
rs12488464	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs12489293	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12489313	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12493521	0.82[EUR][1000 genomes]
rs12495229	0.94[EUR][1000 genomes]
rs12495954	0.96[EUR][1000 genomes]
rs12637913	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12637947	0.90[EUR][1000 genomes]
rs12714670	0.82[EUR][1000 genomes]
rs13066960	0.84[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs13087636	0.84[EUR][1000 genomes]
rs1370212	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1437047	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1437048	0.91[EUR][1000 genomes]
rs1437049	0.95[EUR][1000 genomes]
rs1437055	0.81[EUR][1000 genomes]
rs1583577	0.96[EUR][1000 genomes]
rs1583578	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17364877	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2043685	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2083018	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2118188	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2118189	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2118190	0.91[EUR][1000 genomes]
rs2118191	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2118192	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2164647	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2324795	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28553515	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2875443	0.91[ASN][1000 genomes]
rs28894812	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35309716	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs36015800	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4425259	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4572769	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4855148	0.82[EUR][1000 genomes]
rs4855174	0.82[EUR][1000 genomes]
rs55719700	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56044242	0.83[EUR][1000 genomes]
rs59662471	0.90[EUR][1000 genomes]
rs6775872	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6779214	0.82[EUR][1000 genomes]
rs6781774	0.83[AMR][1000 genomes]
rs6782806	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6807530	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs728179	0.90[EUR][1000 genomes]
rs728180	0.95[EUR][1000 genomes]
rs73133829	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73137958	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73137985	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73139911	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73139914	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73139922	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73139923	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7628864	0.91[EUR][1000 genomes]
rs7630849	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7631441	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs920188	0.82[EUR][1000 genomes]
rs9284805	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs9284807	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9284809	0.84[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9310025	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9310026	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs9310027	0.82[EUR][1000 genomes]
rs9310028	0.88[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9310029	0.88[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs9310030	0.86[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs9310033	0.84[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9310036	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9310037	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9310038	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9310039	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9631517	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9682104	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs9682583	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9682971	0.83[AFR][1000 genomes]
rs9683172	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs9683187	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs9683191	0.84[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9683301	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9683310	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9713014	0.84[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9713018	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9713389	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9713410	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9713421	0.82[EUR][1000 genomes]
rs9713432	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9713574	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs9713693	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9713794	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs9756702	0.85[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9757447	0.88[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs9757801	0.84[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9759006	0.84[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9759053	0.85[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9799281	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs9815344	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9815450	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9816006	0.91[EUR][1000 genomes]
rs9818400	0.96[EUR][1000 genomes]
rs9819570	0.91[EUR][1000 genomes]
rs9819897	0.91[EUR][1000 genomes]
rs9821486	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9826119	0.84[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs9830914	0.87[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs9833108	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9836383	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9841059	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9844776	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9850281	0.90[EUR][1000 genomes]
rs9856526	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs9858833	0.82[AFR][1000 genomes]
rs9859483	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9864625	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9866183	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9868576	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs9881535	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9882953	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs9985323	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9985324	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][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	nsv877116	chr3:86518318-86964922	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv877117	chr3:86665408-86927574	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv877118	chr3:86722823-86927574	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv877119	chr3:86722823-86952516	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv877120	chr3:86722823-86961118	Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats	Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv877121	chr3:86732817-86916882	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv877122	chr3:86732817-86927574	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv877123	chr3:86732817-86952516	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv877125	chr3:86794501-86916882	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
10	nsv877126	chr3:86794501-86927574	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
11	nsv519148	chr3:86831077-86995124	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
12	nsv877127	chr3:86832039-86952516	Flanking Active TSS Weak transcription Active TSS Enhancers ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
13	nsv1008177	chr3:86841615-86905761	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	lncRNA	n/a	inside rSNPs	diseases
14	nsv877128	chr3:86845934-86952516	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	lncRNA	n/a	inside rSNPs	diseases
15	nsv877129	chr3:86845934-86964922	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	lncRNA	n/a	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:86863200-86865200	Enhancers	ES-I3 Cell Line	embryonic stem cell
2	chr3:86863200-86865200	Enhancers	iPS-18 Cell Line	embryonic stem cell
3	chr3:86863200-86865600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:86863400-86865200	Enhancers	iPS-15b Cell Line	embryonic stem cell
5	chr3:86863400-86865800	Enhancers	HUES64 Cell Line	embryonic stem cell
6	chr3:86863600-86865200	Enhancers	NH-A	brain
7	chr3:86863600-86866200	Enhancers	HSMM	muscle
8	chr3:86863800-86865400	Enhancers	H1 Cell Line	embryonic stem cell
9	chr3:86864000-86865400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr3:86864200-86865400	Enhancers	Osteobl	bone
11	chr3:86864200-86865600	Enhancers	Muscle Satellite Cultured Cells	--
12	chr3:86864400-86865400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr3:86864400-86865400	Enhancers	NHLF	lung
14	chr3:86864400-86865600	Enhancers	HSMMtube	muscle
15	chr3:86864400-86866200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr3:86864600-86865400	Enhancers	Fetal Lung	lung
17	chr3:86864600-86866600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr3:86864800-86865600	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr3:86864800-86866200	Enhancers	iPS-20b Cell Line	embryonic stem cell
20	chr3:86864800-86866600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr3:86865000-86866200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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