Variant report

Variant	rs220793
Chromosome Location	chr6:165807502-165807503
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs17193	0.95[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs220749	0.83[ASN][1000 genomes]
rs220752	0.81[CEU][hapmap]
rs220759	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs220761	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs220762	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs220763	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs220764	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs220766	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs220767	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs220768	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.91[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs220769	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs220770	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs220772	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs220774	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs220775	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs220776	0.81[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs220777	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs220778	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs220780	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs220781	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs220784	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs220788	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs220789	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs220790	0.81[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.82[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs220797	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs220798	0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs220799	0.95[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs220800	0.81[CEU][hapmap];0.82[GIH][hapmap]
rs220803	0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs220804	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs220805	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs545605	0.91[ASN][1000 genomes]
rs545609	0.91[ASN][1000 genomes]
rs578592	0.86[CHB][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432982	chr6:165528589-165835589	Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	nsv605245	chr6:165542686-165845903	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
3	nsv1031648	chr6:165544569-165841029	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
4	nsv432983	chr6:165554403-165851585	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
5	esv3417270	chr6:165682773-166023032	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
6	nsv886928	chr6:165722345-166197889	Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv830863	chr6:165803464-165970091	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs220793	PDE10A	cis	cerebellum	SCAN
rs220793	SMOC2	cis	parietal	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:165747600-165853000	Weak transcription	A549	lung
2	chr6:165764400-165813400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:165772000-165835800	Weak transcription	Fetal Kidney	kidney
4	chr6:165787400-165813400	Weak transcription	Fetal Lung	lung
5	chr6:165788000-165856800	Weak transcription	Fetal Muscle Trunk	muscle
6	chr6:165790000-165810600	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr6:165790200-165831400	Weak transcription	Fetal Muscle Leg	muscle
8	chr6:165790400-165811400	Weak transcription	Ovary	ovary
9	chr6:165791400-165834000	Weak transcription	Brain Anterior Caudate	brain
10	chr6:165796000-165813400	Weak transcription	Brain Germinal Matrix	brain
11	chr6:165796400-165823000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr6:165797200-165807600	Weak transcription	Brain Hippocampus Middle	brain
13	chr6:165797800-165809800	Weak transcription	Stomach Smooth Muscle	stomach
14	chr6:165799000-165817600	Weak transcription	Fetal Brain Male	brain
15	chr6:165799200-165808600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr6:165799200-165811800	Weak transcription	Brain Angular Gyrus	brain
17	chr6:165800400-165807600	Strong transcription	HSMM	muscle
18	chr6:165802000-165827200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr6:165802600-165810000	Weak transcription	Pancreas	Pancrea
20	chr6:165802800-165831200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr6:165804200-165828200	Weak transcription	Hela-S3	cervix
22	chr6:165804200-165831400	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr6:165804400-165807600	Weak transcription	Left Ventricle	heart
24	chr6:165804400-165808000	Weak transcription	Fetal Brain Female	brain
25	chr6:165804400-165816600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr6:165804400-165826000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr6:165804400-165827600	Weak transcription	HSMMtube	muscle
28	chr6:165806400-165808600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr6:165806400-165826000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr6:165806400-165862000	Weak transcription	Right Ventricle	heart
31	chr6:165807400-165808000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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