Variant report

Variant	rs9375955
Chromosome Location	chr6:133624410-133624411
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 74 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10457600	1.00[AFR][1000 genomes]
rs10484669	1.00[ASW][hapmap]
rs12173440	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12175835	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12191026	1.00[AFR][1000 genomes]
rs12192839	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12196069	1.00[AFR][1000 genomes]
rs12196492	1.00[AFR][1000 genomes]
rs12199138	1.00[AFR][1000 genomes]
rs12200393	1.00[AFR][1000 genomes]
rs12210216	1.00[AFR][1000 genomes]
rs12211999	1.00[AFR][1000 genomes]
rs12213452	1.00[AFR][1000 genomes]
rs1336520	0.88[CEU][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1415858	0.81[CHD][hapmap];0.81[TSI][hapmap]
rs17301249	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2095602	1.00[ASW][hapmap]
rs2095603	1.00[ASW][hapmap]
rs28405267	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3777796	0.82[AMR][1000 genomes]
rs4278037	0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs5025271	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs55947866	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs56377439	0.82[AMR][1000 genomes]
rs62428563	1.00[AFR][1000 genomes]
rs62428596	1.00[AFR][1000 genomes]
rs62428597	1.00[AFR][1000 genomes]
rs62428664	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62428665	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62428666	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62428668	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62428724	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62428725	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62428726	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62430313	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62430315	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62430317	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62430318	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62430319	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62431672	0.87[ASN][1000 genomes]
rs62431677	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62431680	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62431681	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6919155	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6940510	0.81[ASN][1000 genomes]
rs745091	0.80[CHD][hapmap]
rs7746390	1.00[AFR][1000 genomes]
rs9373043	1.00[CEU][hapmap];0.89[CHB][hapmap];0.91[JPT][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9373044	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9373045	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9373046	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9373047	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9373048	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9375948	0.83[JPT][hapmap]
rs9375949	0.82[AMR][1000 genomes]
rs9385640	0.82[AMR][1000 genomes]
rs9385641	0.82[AMR][1000 genomes]
rs9389059	0.82[AMR][1000 genomes]
rs9389061	0.81[CHD][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap]
rs9389064	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9389066	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9399055	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9399057	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9399058	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9402493	0.81[CHD][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap]
rs9402494	1.00[ASW][hapmap];0.81[CHD][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes]
rs9402497	0.81[CHD][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap]
rs9402501	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9402502	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758080	chr6:133444719-133627364	Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	esv2759470	chr6:133444719-133627364	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv886678	chr6:133550279-133631190	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv886679	chr6:133578733-133635272	Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv886680	chr6:133613759-133663021	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9375955	VDAC2	trans	cerebellum	SCAN
rs9375955	CLYBL	trans	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:133599000-133629000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr6:133613000-133630600	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr6:133613000-133655000	Weak transcription	Hela-S3	cervix
4	chr6:133620800-133626200	Weak transcription	Psoas Muscle	Psoas
5	chr6:133623200-133626200	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr6:133623200-133626200	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr6:133623200-133636200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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