Variant report

Variant	rs1781879
Chromosome Location	chr19:21406087-21406088
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 93 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10416988	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10417249	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10422057	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11665921	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12611085	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12611135	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12976375	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1445847	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1620157	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1645791	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1645804	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1781860	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1781861	0.88[AFR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1781862	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1781880	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1937811	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs193900	0.82[ASN][1000 genomes]
rs2021432	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2042985	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2081183	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2081186	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2081187	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2081188	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2113136	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2259655	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs250002	0.81[ASN][1000 genomes]
rs250003	0.81[ASN][1000 genomes]
rs30109	0.81[ASN][1000 genomes]
rs30111	0.82[ASN][1000 genomes]
rs35915214	0.81[ASN][1000 genomes]
rs4121277	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4280382	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4305209	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4411627	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4468754	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4482412	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4485500	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4493182	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs455492	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4560042	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4606860	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4609982	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs584725	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs594638	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs617145	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs625209	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs634249	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs634661	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs636752	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs637308	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6511209	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6511210	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6511211	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6511212	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6511214	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6511215	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs660551	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs661267	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs663416	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs665561	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs669038	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs673889	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs675130	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs689249	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7245597	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7246432	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7247871	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7247882	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7248088	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7250372	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7251075	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7254835	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7254957	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7257196	0.86[ASN][1000 genomes]
rs7257208	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7259368	0.82[ASN][1000 genomes]
rs7260451	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8111169	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9749536	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3385528	chr19:21030777-21495566	Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	esv3399352	chr19:21232738-21423323	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS 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 miRNA target site	19 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	nsv911414	chr19:21355473-21454672	Enhancers Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv578950	chr19:21388995-21477431	Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv911415	chr19:21388995-21487170	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	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
10	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
11	nsv911418	chr19:21390608-21454672	ZNF genes & repeats Genic enhancers Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv517759	chr19:21391844-21420882	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	nsv911419	chr19:21391844-21487170	Strong transcription Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
14	nsv978788	chr19:21403145-21458328	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1781879	ZNF708	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21404400-21406800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr19:21405400-21407800	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr19:21405800-21406800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr19:21405800-21430000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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