Variant report

Variant	rs494608
Chromosome Location	chr11:63143681-63143682
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:63143315..63147514-chr11:63148756..63151985,3	K562	blood:
2	chr11:63136269..63139132-chr11:63142278..63145159,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000149742	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10750998	0.98[ASN][1000 genomes]
rs10792406	0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs10897383	0.91[CHB][hapmap];0.95[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap]
rs10897384	0.91[CHB][hapmap];0.95[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap]
rs10897396	0.95[CHB][hapmap];0.95[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap]
rs10897397	0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap]
rs10897399	0.95[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.90[MEX][hapmap]
rs10897407	1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap]
rs11231397	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs11231409	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap]
rs11231410	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap]
rs11231411	0.95[CHB][hapmap];0.95[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][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	0.96[ASN][1000 genomes]
rs1193726	1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap]
rs1193733	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1193786	0.86[ASN][1000 genomes]
rs1193787	0.90[ASN][1000 genomes]
rs1193891	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap]
rs1193892	0.95[CHB][hapmap];0.95[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap]
rs1193904	0.82[AFR][1000 genomes]
rs1201559	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap]
rs12283500	0.95[ASN][1000 genomes]
rs12293171	0.90[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]
rs1404608	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap]
rs1525064	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs1525071	0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs1723219	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1790218	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap]
rs1790226	0.90[ASN][1000 genomes]
rs1944086	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2317089	0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs2510590	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs2958546	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3891629	0.90[CHB][hapmap];0.95[CHD][hapmap]
rs3915142	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4121881	0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4445638	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap]
rs471044	0.94[ASN][1000 genomes]
rs474096	1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs474874	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs483012	1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap]
rs486460	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs488803	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4963385	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap]
rs4963405	0.96[ASN][1000 genomes]
rs499003	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs502642	0.95[ASN][1000 genomes]
rs505653	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs510547	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs511480	0.98[ASN][1000 genomes]
rs513338	1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs515213	1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs516536	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs517655	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs526686	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs532085	1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap]
rs534799	1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs537194	0.81[AFR][1000 genomes]
rs538309	0.88[AMR][1000 genomes]
rs543429	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs549144	1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs556730	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs557658	1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs557879	1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs558472	0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs563948	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs564917	0.90[ASN][1000 genomes]
rs566456	0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs572017	0.82[AFR][1000 genomes]
rs575009	0.91[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs6591778	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs688999	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7126435	0.95[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap]
rs722508	1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs7949840	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][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	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs494608	DNAJC4	cis	parietal	SCAN
rs494608	ACTN3	cis	cerebellum	SCAN
rs494608	SDHAF2	cis	parietal	SCAN
rs494608	CD6	cis	cerebellum	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	chr11:63142600-63147000	Strong transcription	Liver	Liver

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