Variant report

Variant	rs4468754
Chromosome Location	chr19:21431997-21431998
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 93 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10416988	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10417249	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10422057	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11665921	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12611085	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12611135	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12976375	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1445847	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1620157	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1645791	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1645804	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1781860	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1781861	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1781862	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1781879	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1781880	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1937811	0.87[EUR][1000 genomes]
rs2021432	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2042985	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2081183	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2081186	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2081187	0.86[EUR][1000 genomes]
rs2081188	0.86[EUR][1000 genomes]
rs2113136	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2259655	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs250003	0.88[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap]
rs29727	0.85[CEU][hapmap];0.86[TSI][hapmap]
rs29730	0.85[CEU][hapmap]
rs35915214	0.92[ASN][1000 genomes]
rs388229	0.82[CHB][hapmap]
rs4121277	0.90[EUR][1000 genomes]
rs4280382	0.87[EUR][1000 genomes]
rs4305209	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4411627	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4482412	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4485500	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4493182	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs455492	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4560042	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4606860	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4609982	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57740	0.86[CHB][hapmap];0.81[CHD][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.84[ASN][1000 genomes]
rs584725	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs594638	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs606174	0.84[ASN][1000 genomes]
rs606958	0.84[ASN][1000 genomes]
rs617145	0.90[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs625209	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs634249	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs634661	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs636752	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs637308	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6511209	0.86[EUR][1000 genomes]
rs6511210	0.86[EUR][1000 genomes]
rs6511211	0.86[EUR][1000 genomes]
rs6511212	0.86[EUR][1000 genomes]
rs6511214	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6511215	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs660551	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs661267	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs663416	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs665561	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs669038	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs673889	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs675130	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs689249	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs694208	0.84[ASN][1000 genomes]
rs7245597	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7246432	0.86[EUR][1000 genomes]
rs7247871	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7247882	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7248088	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7250372	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.84[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7251075	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7254835	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7254957	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7257208	0.86[EUR][1000 genomes]
rs7259520	0.85[CEU][hapmap];0.81[TSI][hapmap]
rs7260451	0.86[EUR][1000 genomes]
rs8111169	0.86[EUR][1000 genomes]
rs9630897	0.85[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 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	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs4468754	ZNF493	cis	cerebellum	SCAN
rs4468754	TSSK6	cis	parietal	SCAN
rs4468754	ZNF493	cis	parietal	SCAN
rs4468754	ZNF738	cis	cerebellum	SCAN
rs4468754	PGPEP1	cis	parietal	SCAN
rs4468754	ZNF708	cis	cerebellum	SCAN
rs4468754	ZNF708	cis	Muscle Skeletal	GTEx
rs4468754	LRRC25	cis	parietal	SCAN
rs4468754	ZNF493	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21430400-21436200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr19:21430400-21436200	Weak transcription	Ovary	ovary
3	chr19:21431800-21432400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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