Variant report

Variant	rs12971724
Chromosome Location	chr19:21611948-21611949
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 97 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs12150996	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12151067	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12151068	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12151222	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12975330	0.80[ASN][1000 genomes]
rs12975981	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12976011	0.80[ASN][1000 genomes]
rs12981869	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12984238	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1566474	0.80[ASN][1000 genomes]
rs1566476	0.80[ASN][1000 genomes]
rs1566477	0.80[ASN][1000 genomes]
rs16997924	0.80[ASN][1000 genomes]
rs17618715	0.80[ASN][1000 genomes]
rs17618778	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1762580	0.80[ASN][1000 genomes]
rs2262897	0.80[ASN][1000 genomes]
rs2562457	0.80[ASN][1000 genomes]
rs2562458	0.80[ASN][1000 genomes]
rs2562459	0.80[ASN][1000 genomes]
rs2650775	0.82[EUR][1000 genomes]
rs2650778	0.80[ASN][1000 genomes]
rs2650780	0.80[ASN][1000 genomes]
rs2650781	0.80[ASN][1000 genomes]
rs2650782	0.80[ASN][1000 genomes]
rs2650783	0.80[ASN][1000 genomes]
rs2650785	0.80[ASN][1000 genomes]
rs2650786	0.80[ASN][1000 genomes]
rs2650808	0.80[ASN][1000 genomes]
rs28839521	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2914636	0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2914637	0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2914647	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2928210	0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2937161	0.83[EUR][1000 genomes]
rs2968081	0.80[ASN][1000 genomes]
rs34560125	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34875588	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs35148123	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35245030	0.80[ASN][1000 genomes]
rs35578515	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35860067	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4332859	0.80[ASN][1000 genomes]
rs483383	0.80[ASN][1000 genomes]
rs501647	0.80[ASN][1000 genomes]
rs509540	0.80[ASN][1000 genomes]
rs549882	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs552039	0.80[ASN][1000 genomes]
rs56152627	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs566230	0.80[ASN][1000 genomes]
rs57055133	0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs57841525	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58121117	0.80[ASN][1000 genomes]
rs59617671	0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs608002	0.80[ASN][1000 genomes]
rs62107470	0.80[ASN][1000 genomes]
rs62107538	0.80[ASN][1000 genomes]
rs62109224	0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs62110379	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62111469	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62111470	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62111472	0.80[ASN][1000 genomes]
rs62111476	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6511247	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs670813	0.80[ASN][1000 genomes]
rs67723811	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs685844	0.80[ASN][1000 genomes]
rs7245848	0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7246684	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7248700	0.80[AMR][1000 genomes]
rs7257584	0.86[ASN][1000 genomes]
rs7258211	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7258523	0.83[ASN][1000 genomes]
rs7259178	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73025767	0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs8099863	0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs8101077	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8101442	0.80[ASN][1000 genomes]
rs8102655	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8103151	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8105404	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8105629	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8107042	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8107940	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8110230	0.82[EUR][1000 genomes]
rs8111189	0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs8112359	0.83[ASN][1000 genomes]
rs8113558	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3518033	chr19:21278465-21747567	Strong transcription Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	esv3518034	chr19:21278465-21747567	ZNF genes & repeats Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	esv3414204	chr19:21301761-21839451	ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv3325271	chr19:21445407-21792817	Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv911420	chr19:21454672-21613397	ZNF genes & repeats Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	esv2751783	chr19:21465822-21726337	Strong transcription ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
7	esv3363678	chr19:21483148-21756908	Strong transcription Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
8	nsv578952	chr19:21535707-21868584	Genic enhancers Active TSS ZNF genes & repeats Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
9	nsv911421	chr19:21579718-21613397	Strong transcription Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	n/a

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12971724	ZNF429	cis	Artery Aorta	GTEx
rs12971724	ZNF429	cis	Whole Blood	GTEx
rs12971724	ZNF493	Cis_1M	lymphoblastoid	RTeQTL
rs12971724	ZNF738	cis	Adipose Subcutaneous	GTEx
rs12971724	ZNF738	Cis_1M	lymphoblastoid	RTeQTL
rs12971724	ZNF738	cis	Thyroid	GTEx

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21585000-21614000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr19:21600000-21613000	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr19:21607600-21630200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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