Variant report

Variant	rs10420891
Chromosome Location	chr19:38320539-38320540
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SIPA1L3-1	chr19:38320191-38322797	ENSG00000229481

Extended variants
information (count: 98 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs10048511	0.80[EUR][1000 genomes]
rs10401637	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10401968	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10402530	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10404567	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.82[EUR][1000 genomes]
rs10409402	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10409487	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10415548	0.88[CEU][hapmap]
rs10420746	1.00[CEU][hapmap];0.81[CHB][hapmap]
rs10427125	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11083432	1.00[CEU][hapmap];0.88[GIH][hapmap];0.92[TSI][hapmap]
rs1119229	0.88[CEU][hapmap];0.83[GIH][hapmap]
rs11878269	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11879180	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1291	1.00[CEU][hapmap];0.81[CHB][hapmap];0.93[GIH][hapmap];0.96[TSI][hapmap]
rs12974225	1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[GIH][hapmap];0.89[MEX][hapmap];0.96[TSI][hapmap]
rs12975057	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12979640	1.00[CEU][hapmap];0.81[CHB][hapmap];0.88[GIH][hapmap];0.92[TSI][hapmap]
rs1643466	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap]
rs1643467	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap]
rs1643468	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs16958861	0.93[CEU][hapmap];0.81[CHB][hapmap]
rs16958863	0.83[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.88[GIH][hapmap];0.89[MEX][hapmap];0.96[TSI][hapmap]
rs171376	0.83[EUR][1000 genomes]
rs1725481	1.00[CEU][hapmap];0.80[JPT][hapmap]
rs1725482	1.00[CEU][hapmap];0.80[JPT][hapmap];0.92[TSI][hapmap]
rs1725499	0.88[CEU][hapmap]
rs2068431	0.85[ASN][1000 genomes]
rs2075281	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2287229	1.00[CEU][hapmap];0.81[CHB][hapmap];0.88[GIH][hapmap];0.89[MEX][hapmap];0.96[TSI][hapmap]
rs241932	1.00[CEU][hapmap];0.81[CHB][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];0.89[MEX][hapmap];0.96[TSI][hapmap];0.83[EUR][1000 genomes]
rs241950	0.83[EUR][1000 genomes]
rs2909088	0.83[ASW][hapmap];0.81[CHB][hapmap];0.82[GIH][hapmap];0.89[MEX][hapmap];0.83[TSI][hapmap]
rs2909093	0.83[ASW][hapmap];0.94[CEU][hapmap];0.81[CHB][hapmap];0.91[GIH][hapmap];0.92[TSI][hapmap]
rs2909098	0.83[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.91[GIH][hapmap];0.89[MEX][hapmap];0.96[TSI][hapmap]
rs2909102	0.83[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.88[GIH][hapmap];0.89[MEX][hapmap];0.96[TSI][hapmap]
rs2909105	1.00[CEU][hapmap];0.81[CHB][hapmap];0.86[GIH][hapmap];0.96[TSI][hapmap]
rs2909109	0.83[ASW][hapmap];0.81[CHB][hapmap];0.82[GIH][hapmap];0.89[MEX][hapmap];0.83[TSI][hapmap]
rs2927739	1.00[CEU][hapmap];0.81[CHB][hapmap]
rs2927740	0.83[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.88[GIH][hapmap];0.96[TSI][hapmap]
rs2927747	0.83[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.88[GIH][hapmap];0.89[MEX][hapmap];0.96[TSI][hapmap]
rs2972437	0.83[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.91[GIH][hapmap];0.89[MEX][hapmap];0.96[TSI][hapmap]
rs2972438	0.83[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.91[GIH][hapmap];0.89[MEX][hapmap];0.96[TSI][hapmap]
rs2972439	0.83[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.91[GIH][hapmap];0.89[MEX][hapmap];0.96[TSI][hapmap]
rs2972447	1.00[CEU][hapmap];0.81[CHB][hapmap]
rs2972448	0.83[ASW][hapmap];0.81[CHB][hapmap];0.82[GIH][hapmap];0.89[MEX][hapmap];0.83[TSI][hapmap]
rs3095726	0.93[CEU][hapmap];0.81[CHB][hapmap]
rs35209753	0.84[EUR][1000 genomes]
rs353410	0.88[CEU][hapmap]
rs353411	0.88[CEU][hapmap]
rs353414	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap]
rs353415	1.00[CEU][hapmap]
rs353423	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.85[YRI][hapmap]
rs3786869	0.87[CEU][hapmap]
rs3848626	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3910952	0.81[ASN][1000 genomes]
rs4239516	0.87[CEU][hapmap]
rs4802135	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4803509	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4803524	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4803528	0.85[ASN][1000 genomes]
rs4803551	0.88[CEU][hapmap]
rs4803573	0.88[CEU][hapmap]
rs58449039	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6508742	0.86[EUR][1000 genomes]
rs705491	0.88[CEU][hapmap]
rs705492	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap]
rs705493	0.88[CEU][hapmap]
rs705494	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs705495	0.88[CEU][hapmap]
rs7245864	0.84[ASN][1000 genomes]
rs7250409	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs7250571	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7250868	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7252010	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7257125	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7258597	0.82[EUR][1000 genomes]
rs8101752	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8101858	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8102579	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8104076	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8110284	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs8112706	1.00[CEU][hapmap];0.81[CHB][hapmap];0.82[EUR][1000 genomes]
rs8113521	0.88[CEU][hapmap]
rs8182498	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs833895	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap]
rs833914	0.80[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.88[TSI][hapmap]
rs833926	1.00[CEU][hapmap]
rs856300	0.94[CEU][hapmap];0.81[CHB][hapmap];0.93[GIH][hapmap];0.89[MEX][hapmap];0.96[TSI][hapmap];0.82[EUR][1000 genomes]
rs856304	1.00[CEU][hapmap];0.81[CHB][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];0.89[MEX][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes]
rs9304569	0.86[EUR][1000 genomes]
rs9304572	0.81[EUR][1000 genomes]
rs958305	1.00[CEU][hapmap];0.88[GIH][hapmap];0.96[TSI][hapmap]
rs968073	1.00[CEU][hapmap];0.81[CHB][hapmap];0.88[GIH][hapmap];0.89[MEX][hapmap];0.96[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv833820	chr19:38190721-38414049	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv1057428	chr19:38282158-38320814	Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1062040	chr19:38294465-38370456	Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs10420891	HIPK4	cis	cerebellum	SCAN
rs10420891	PHLDB3	cis	parietal	SCAN
rs10420891	CBLC	cis	parietal	SCAN
rs10420891	WDR87	cis	Thyroid	GTEx
rs10420891	ZNF571	cis	multi-tissue	Pritchard
rs10420891	DMPK	cis	parietal	SCAN
rs10420891	PAFAH1B3	cis	cerebellum	SCAN
rs10420891	PHLDB3	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38312000-38324000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
2	chr19:38314000-38321600	ZNF genes & repeats	Fetal Lung	lung
3	chr19:38314400-38324600	ZNF genes & repeats	Adipose Nuclei	Adipose
4	chr19:38319600-38324800	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell

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