Variant report

Variant	rs9373046
Chromosome Location	chr6:133621996-133621997
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs12173440	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12175835	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1336520	0.88[CEU][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1415858	0.82[CHD][hapmap];0.80[TSI][hapmap]
rs17301249	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28405267	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4278037	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs5025271	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs62428664	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62428665	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62428666	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62428668	0.88[EUR][1000 genomes]
rs62428724	0.88[EUR][1000 genomes]
rs62428725	0.88[EUR][1000 genomes]
rs62428726	0.88[EUR][1000 genomes]
rs62430313	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62430315	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62430317	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62430318	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62430319	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62431677	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62431680	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62431681	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6919155	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9373043	1.00[CEU][hapmap];0.89[CHB][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9373044	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9373045	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9373047	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9373048	1.00[CHB][hapmap];0.93[CHD][hapmap];0.81[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9375955	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]
rs9389061	0.86[CHD][hapmap];0.91[MEX][hapmap];0.80[TSI][hapmap]
rs9389064	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9389066	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9399055	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9399057	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9399058	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9402493	0.86[CHD][hapmap];0.83[MEX][hapmap];0.80[TSI][hapmap]
rs9402494	0.86[CHD][hapmap];0.91[MEX][hapmap];0.80[TSI][hapmap]
rs9402497	0.86[CHD][hapmap];0.83[MEX][hapmap];0.80[TSI][hapmap]
rs9402501	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9402502	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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
rs9373046	VDAC2	trans	cerebellum	SCAN
rs9373046	CLYBL	trans	parietal	SCAN

Chromatin state (count:10 , 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	chr6:133620400-133622600	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr6:133620400-133622800	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr6:133620800-133623000	Weak transcription	Left Ventricle	heart
7	chr6:133620800-133626200	Weak transcription	Psoas Muscle	Psoas
8	chr6:133621600-133622000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr6:133621600-133623000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr6:133621800-133623200	Enhancers	Muscle Satellite Cultured Cells	--

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