Variant report

Variant	rs10402530
Chromosome Location	chr19:38321638-38321639
allele	C/T
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: 97 )
Associated
traits (count: 8 )

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

rs_ID	r²[population]
rs10048511	0.80[EUR][1000 genomes]
rs10401637	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10401968	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10404567	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs10409402	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10409487	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10415548	0.88[CEU][hapmap]
rs10420746	1.00[CEU][hapmap];0.81[CHB][hapmap]
rs10420891	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10427125	0.93[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	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11879180	0.97[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	0.97[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	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];0.85[YRI][hapmap];0.90[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	0.81[CHB][hapmap];0.82[GIH][hapmap];0.89[MEX][hapmap];0.83[TSI][hapmap]
rs2909093	0.94[CEU][hapmap];0.81[CHB][hapmap];0.91[GIH][hapmap];0.92[TSI][hapmap]
rs2909098	1.00[CEU][hapmap];0.81[CHB][hapmap];0.91[GIH][hapmap];0.89[MEX][hapmap];0.96[TSI][hapmap]
rs2909102	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	0.81[CHB][hapmap];0.82[GIH][hapmap];0.89[MEX][hapmap];0.83[TSI][hapmap]
rs2927739	1.00[CEU][hapmap];0.81[CHB][hapmap]
rs2927740	1.00[CEU][hapmap];0.81[CHB][hapmap];0.88[GIH][hapmap];0.96[TSI][hapmap]
rs2927747	1.00[CEU][hapmap];0.81[CHB][hapmap];0.88[GIH][hapmap];0.89[MEX][hapmap];0.96[TSI][hapmap]
rs2972437	1.00[CEU][hapmap];0.81[CHB][hapmap];0.91[GIH][hapmap];0.89[MEX][hapmap];0.96[TSI][hapmap]
rs2972438	1.00[CEU][hapmap];0.81[CHB][hapmap];0.91[GIH][hapmap];0.89[MEX][hapmap];0.96[TSI][hapmap]
rs2972439	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	0.81[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];0.82[YRI][hapmap]
rs353415	1.00[CEU][hapmap]
rs353423	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.82[YRI][hapmap]
rs3786869	0.87[CEU][hapmap]
rs3848626	0.99[AFR][1000 genomes];0.95[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[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4803509	0.96[AFR][1000 genomes];0.93[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];0.85[YRI][hapmap];0.92[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	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6508742	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs705491	0.88[CEU][hapmap]
rs705492	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs705493	0.88[CEU][hapmap]
rs705494	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.81[EUR][1000 genomes]
rs705495	0.88[CEU][hapmap]
rs7245864	0.84[ASN][1000 genomes]
rs7250409	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.81[EUR][1000 genomes]
rs7250571	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7250868	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7252010	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7257125	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7258597	0.82[EUR][1000 genomes]
rs8101752	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8101858	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8102579	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8104076	0.89[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]
rs8112706	1.00[CEU][hapmap];0.81[CHB][hapmap];0.82[EUR][1000 genomes]
rs8113521	0.88[CEU][hapmap]
rs8182498	0.97[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	0.84[ASW][hapmap];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	0.80[AMR][1000 genomes];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:3 , 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	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
rs10402530	DMPK	cis	parietal	SCAN
rs10402530	ZNF571	cis	multi-tissue	Pritchard
rs10402530	HIPK4	cis	cerebellum	SCAN
rs10402530	PHLDB3	cis	cerebellum	SCAN
rs10402530	PAFAH1B3	cis	cerebellum	SCAN
rs10402530	PHLDB3	cis	parietal	SCAN
rs10402530	CBLC	cis	parietal	SCAN
rs10402530	WDR87	cis	Thyroid	GTEx

Chromatin state (count:3 , 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	chr19:38314400-38324600	ZNF genes & repeats	Adipose Nuclei	Adipose
3	chr19:38319600-38324800	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell

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