Variant report

Variant	rs406900
Chromosome Location	chr6:88085447-88085448
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 75 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs1051550	1.00[JPT][hapmap]
rs11964198	0.92[JPT][hapmap]
rs11964212	0.92[JPT][hapmap]
rs11964237	0.86[CHD][hapmap];0.92[JPT][hapmap];0.86[MEX][hapmap]
rs11966859	0.92[JPT][hapmap]
rs1203155	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1203156	0.84[ASW][hapmap];0.88[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1209113	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12529410	0.86[CHD][hapmap];0.92[JPT][hapmap];0.81[MEX][hapmap]
rs12529423	0.85[CHD][hapmap];0.92[JPT][hapmap];0.86[MEX][hapmap]
rs12663865	0.86[CHD][hapmap];0.92[JPT][hapmap];0.86[MEX][hapmap]
rs13211410	0.92[JPT][hapmap]
rs13217485	0.86[CHD][hapmap];0.92[JPT][hapmap];0.86[MEX][hapmap]
rs173334	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1884320	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs242271	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs242272	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs242273	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs242291	0.82[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs242292	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs242293	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3736740	0.92[JPT][hapmap]
rs414013	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4329082	0.92[JPT][hapmap]
rs4707365	0.92[JPT][hapmap]
rs4707367	0.86[CHD][hapmap];0.92[JPT][hapmap];0.90[MEX][hapmap]
rs4707369	0.92[EUR][1000 genomes]
rs6454611	0.92[JPT][hapmap]
rs6454612	1.00[JPT][hapmap]
rs6454613	0.92[JPT][hapmap]
rs6454616	0.86[CHD][hapmap];0.92[JPT][hapmap];0.86[MEX][hapmap]
rs6454618	0.86[CHD][hapmap];0.92[JPT][hapmap];0.86[MEX][hapmap]
rs6454622	0.92[JPT][hapmap]
rs6454623	0.92[JPT][hapmap]
rs6454624	0.92[JPT][hapmap]
rs6454625	0.86[CHD][hapmap];0.92[JPT][hapmap];0.86[MEX][hapmap]
rs6454626	0.92[JPT][hapmap]
rs6900397	0.86[CHD][hapmap];0.92[JPT][hapmap];0.90[MEX][hapmap]
rs6907825	0.86[CHD][hapmap];0.92[JPT][hapmap];0.91[MEX][hapmap]
rs6909168	0.92[JPT][hapmap]
rs6910429	0.86[CHD][hapmap];0.92[JPT][hapmap];0.86[MEX][hapmap]
rs6912282	0.92[JPT][hapmap]
rs6912875	0.92[JPT][hapmap]
rs6915562	0.86[CHD][hapmap];0.92[JPT][hapmap];0.86[MEX][hapmap]
rs6919775	0.92[JPT][hapmap]
rs6930072	0.92[JPT][hapmap]
rs6930076	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6940716	0.86[CHD][hapmap];0.82[GIH][hapmap];0.92[JPT][hapmap];0.86[TSI][hapmap]
rs694524	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7744338	0.82[CEU][hapmap];0.86[CHD][hapmap];0.90[GIH][hapmap];0.92[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7744793	0.92[JPT][hapmap]
rs7746469	0.92[JPT][hapmap]
rs7746876	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7749047	1.00[JPT][hapmap]
rs7749162	0.91[JPT][hapmap]
rs7753821	0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs7764963	0.92[JPT][hapmap]
rs7766462	0.92[JPT][hapmap]
rs7767220	1.00[JPT][hapmap]
rs7773804	0.92[JPT][hapmap]
rs926946	1.00[JPT][hapmap]
rs9294377	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9342112	0.92[ASN][1000 genomes]
rs9344708	0.92[JPT][hapmap]
rs9353484	1.00[JPT][hapmap]
rs9362426	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9362428	0.92[JPT][hapmap]
rs9450662	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9450672	0.92[JPT][hapmap]
rs9450674	0.92[JPT][hapmap]
rs9450675	0.92[JPT][hapmap]
rs9450676	0.92[JPT][hapmap]
rs9450682	0.86[CHD][hapmap];0.82[GIH][hapmap];0.92[JPT][hapmap];0.86[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018155	chr6:88049729-88272862	Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv830722	chr6:88054186-88223625	Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs406900	C6orf162	cis	parietal	SCAN
rs406900	C6orf165	cis	parietal	SCAN
rs406900	C6orf165	cis	cerebellum	SCAN
rs406900	C6orf162	cis	cerebellum	SCAN
rs406900	C6orf162	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:88040600-88116800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr6:88054800-88110200	Weak transcription	Primary T cells from cord blood	blood
3	chr6:88061600-88094600	Weak transcription	Left Ventricle	heart
4	chr6:88080200-88093800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr6:88083600-88088800	Weak transcription	Aorta	Aorta
6	chr6:88083800-88086000	Weak transcription	Psoas Muscle	Psoas
7	chr6:88084600-88085600	Enhancers	HMEC	breast

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