Variant report

Variant	rs608002
Chromosome Location	chr19:21513408-21513409
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 76 )
Associated
traits (count: 10 )

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

rs_ID	r²[population]
rs11085443	0.84[EUR][1000 genomes]
rs11671832	0.82[ASN][1000 genomes]
rs12151067	0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12151068	0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12971724	0.80[ASN][1000 genomes]
rs12975981	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12981869	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12984238	0.80[ASN][1000 genomes]
rs1678822	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17618715	1.00[ASN][1000 genomes]
rs17618778	0.80[ASN][1000 genomes]
rs1762580	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17680671	0.89[ASN][1000 genomes]
rs1781863	0.82[EUR][1000 genomes]
rs1813234	0.84[EUR][1000 genomes]
rs1827225	0.86[ASN][1000 genomes]
rs2358984	0.81[EUR][1000 genomes]
rs28839521	0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2914636	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2914637	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2928210	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34560125	0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs34875588	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35148123	0.80[ASN][1000 genomes]
rs35578515	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs35860067	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs483383	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs488125	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs501647	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs504280	0.90[EUR][1000 genomes]
rs509540	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs514390	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs531283	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs549882	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs552039	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs565406	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs566230	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57055133	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58121117	1.00[ASN][1000 genomes]
rs59617671	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs617186	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62107470	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62107538	1.00[ASN][1000 genomes]
rs62109224	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62110379	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs635730	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6511228	0.81[EUR][1000 genomes]
rs670813	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67723811	0.80[ASN][1000 genomes]
rs685844	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7245848	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7246684	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7248700	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7252873	0.81[EUR][1000 genomes]
rs7254762	0.89[ASN][1000 genomes]
rs7258086	0.81[EUR][1000 genomes]
rs73025767	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8099863	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8102328	0.81[EUR][1000 genomes]
rs8103411	0.85[ASN][1000 genomes]
rs8103417	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8105404	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8110470	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8111189	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8113558	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	nsv911416	chr19:21388995-21548211	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv911417	chr19:21388995-21564001	Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	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
7	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
8	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
9	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
10	nsv963023	chr19:21491992-21570395	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	esv3415719	chr19:21511760-21519079	Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs608002	ZNF429	cis	Whole Blood	GTEx
rs608002	ZNF738	cis	Esophagus Muscularis	GTEx
rs608002	CTD-2561J22.5	cis	Thyroid	GTEx
rs608002	CTD-2561J22.5	cis	Adipose Subcutaneous	GTEx
rs608002	ZNF738	cis	Adipose Subcutaneous	GTEx
rs608002	ZNF738	Cis_1M	lymphoblastoid	RTeQTL
rs608002	ZNF738	cis	Thyroid	GTEx
rs608002	ZNF738	cis	Artery Tibial	GTEx
rs608002	ZNF493	Cis_1M	lymphoblastoid	RTeQTL
rs608002	ZNF738	cis	Nerve Tibial	GTEx

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21512400-21513600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr19:21512400-21513600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr19:21512400-21515000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr19:21513400-21513800	ZNF genes & repeats	Dnd41	blood

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