Variant report

Variant	rs12489078
Chromosome Location	chr3:88712390-88712391
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10511138	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11128053	0.84[ASN][1000 genomes]
rs12486895	0.82[ASN][1000 genomes]
rs12487385	0.82[ASN][1000 genomes]
rs12487560	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12487623	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12488032	0.82[ASN][1000 genomes]
rs12488286	0.84[ASN][1000 genomes]
rs12488396	0.84[ASN][1000 genomes]
rs12490357	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12491633	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12491766	0.84[ASN][1000 genomes]
rs12494001	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12495558	0.82[ASN][1000 genomes]
rs12629360	0.84[ASN][1000 genomes]
rs12630722	0.85[EUR][1000 genomes]
rs12633026	0.85[EUR][1000 genomes]
rs12635866	0.89[EUR][1000 genomes]
rs12637931	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12639499	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13073581	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13321865	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17559821	0.90[AFR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17560386	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1979751	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2132362	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28447483	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28784899	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55694746	0.82[ASN][1000 genomes]
rs56076642	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56076980	0.82[ASN][1000 genomes]
rs56302725	0.85[EUR][1000 genomes]
rs56359806	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59752267	0.84[ASN][1000 genomes]
rs59757044	0.90[AFR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60418303	0.84[ASN][1000 genomes]
rs60574566	0.84[ASN][1000 genomes]
rs61176217	0.84[ASN][1000 genomes]
rs6551350	0.84[ASN][1000 genomes]
rs67260046	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs67616120	0.86[EUR][1000 genomes]
rs6776183	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6777020	0.85[EUR][1000 genomes]
rs6778723	0.82[ASN][1000 genomes]
rs6794212	0.84[ASN][1000 genomes]
rs6799848	0.84[ASN][1000 genomes]
rs6802531	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73134314	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73134400	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73136414	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73136419	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73146499	0.82[ASN][1000 genomes]
rs73150566	0.81[EUR][1000 genomes]
rs73150570	0.82[EUR][1000 genomes]
rs73150583	0.83[EUR][1000 genomes]
rs73152336	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7430981	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7431312	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7431370	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7432988	0.84[ASN][1000 genomes]
rs7433029	0.84[ASN][1000 genomes]
rs7637716	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7652836	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9824652	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9856843	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916330	chr3:88083580-88884125	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1014703	chr3:88623532-88733631	Enhancers Weak transcription ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv877156	chr3:88690163-88803526	Weak transcription Enhancers ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv877157	chr3:88690163-88974863	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv1009261	chr3:88700735-88754260	Weak transcription Enhancers Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv536636	chr3:88700735-88754260	Enhancers Weak transcription ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv965408	chr3:88700788-88716041	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:88710000-88713400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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