Variant report

Variant	rs4963405
Chromosome Location	chr11:63148736-63148737
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HRASLS5-3	chr11:63148132-63151901	ucscGeneNc_uc001nxj_1

Extended variants
information (count: 92 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10750998	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10792406	0.91[CHB][hapmap];0.95[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap]
rs10897383	0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs10897384	0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs10897396	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs10897397	0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap]
rs10897399	0.95[CHB][hapmap];0.95[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap]
rs10897407	0.87[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.95[MEX][hapmap];0.84[YRI][hapmap]
rs10897411	0.89[AFR][1000 genomes]
rs11231397	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs11231409	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs11231410	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs11231411	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs11231412	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs11231413	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1152244	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11605137	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1193718	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1193726	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs1193729	0.81[EUR][1000 genomes]
rs1193733	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1193786	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1193787	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1193789	0.83[EUR][1000 genomes]
rs1193891	1.00[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap]
rs1193892	0.95[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap]
rs1201559	0.81[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1205166	0.83[EUR][1000 genomes]
rs1205186	0.83[EUR][1000 genomes]
rs12283500	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12293171	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12574223	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1300798	0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap]
rs1404608	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1525064	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs1525071	0.91[CHB][hapmap];0.95[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap]
rs1608760	0.83[EUR][1000 genomes]
rs1723213	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1723219	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1783634	0.81[EUR][1000 genomes]
rs1789327	0.82[EUR][1000 genomes]
rs1789334	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1790218	0.81[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs1790226	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1944086	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2317089	0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap]
rs2510590	0.95[CHB][hapmap];0.95[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]
rs2958546	0.90[ASN][1000 genomes]
rs3891629	0.90[CHB][hapmap];0.95[CHD][hapmap];0.86[MEX][hapmap]
rs3915142	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4085831	0.82[AFR][1000 genomes]
rs4121881	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4445638	0.87[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.82[YRI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs471044	0.97[ASN][1000 genomes]
rs474096	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap]
rs474874	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs483012	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap]
rs486460	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs488803	0.92[ASN][1000 genomes]
rs494608	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4963385	1.00[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap]
rs499003	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs502642	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs505653	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs510547	0.94[ASN][1000 genomes]
rs511480	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs513338	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap]
rs515213	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap]
rs516536	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs517655	0.92[ASN][1000 genomes]
rs532085	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap]
rs534799	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap]
rs543429	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap]
rs549144	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap]
rs556730	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs557658	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap]
rs557879	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap]
rs558472	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs563948	0.98[ASN][1000 genomes]
rs564917	0.87[ASN][1000 genomes]
rs566456	0.94[ASN][1000 genomes]
rs575009	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap]
rs6591778	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs688999	0.99[ASN][1000 genomes]
rs7126435	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs7130728	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs722508	1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap]
rs7949840	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][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	nsv1051171	chr11:62987064-63835715	Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
2	nsv1053585	chr11:63057767-63180308	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv555178	chr11:63078742-63197930	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	esv1822068	chr11:63146055-63239984	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs4963405	SCGB2A2	cis	parietal	SCAN
rs4963405	DKFZp761E198	cis	parietal	SCAN
rs4963405	STX5	cis	parietal	SCAN
rs4963405	SLC22A10	cis	Esophagus Muscularis	GTEx
rs4963405	DNAJC4	cis	parietal	SCAN
rs4963405	EFEMP2	cis	parietal	SCAN
rs4963405	CTSF	cis	parietal	SCAN
rs4963405	ACTN3	cis	cerebellum	SCAN
rs4963405	SDHAF2	cis	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:63141400-63153200	Weak transcription	HepG2	liver
2	chr11:63148600-63152200	Strong transcription	Liver	Liver

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