Variant report

Variant	rs1838100
Chromosome Location	chr17:66829848-66829849
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1373066	1.00[YRI][hapmap];0.97[AMR][1000 genomes]
rs1443259	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1443261	0.84[ASW][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.94[AMR][1000 genomes]
rs1443262	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1443263	0.90[EUR][1000 genomes]
rs1470292	0.97[AMR][1000 genomes]
rs1470293	0.97[AMR][1000 genomes]
rs1470294	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1481	0.84[CEU][hapmap];0.80[GIH][hapmap];0.84[TSI][hapmap]
rs1550646	0.99[EUR][1000 genomes]
rs17742923	1.00[CHD][hapmap]
rs1808919	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1838101	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1867235	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1899576	0.91[EUR][1000 genomes]
rs1978962	0.96[EUR][1000 genomes]
rs2083790	0.84[AMR][1000 genomes]
rs2218350	1.00[YRI][hapmap];0.97[AMR][1000 genomes]
rs2363753	0.84[AMR][1000 genomes]
rs4246431	0.84[ASW][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.94[AMR][1000 genomes]
rs4556855	0.94[EUR][1000 genomes]
rs4968826	1.00[YRI][hapmap];0.91[AMR][1000 genomes]
rs4968962	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4968967	1.00[MEX][hapmap];0.81[AMR][1000 genomes]
rs6501766	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6501767	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6501768	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6501799	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6501813	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6501835	0.97[AMR][1000 genomes]
rs6501839	0.84[ASW][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes]
rs7209220	0.86[AMR][1000 genomes]
rs7210022	0.86[AMR][1000 genomes]
rs7211979	1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes]
rs7216817	0.80[AMR][1000 genomes]
rs8068204	1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.86[AMR][1000 genomes]
rs8074944	0.86[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes]
rs8078168	0.96[EUR][1000 genomes]
rs8080098	0.84[ASW][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes]
rs8082619	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs894593	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs894594	1.00[YRI][hapmap];0.97[AMR][1000 genomes]
rs980423	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9895868	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]

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	nsv1067334	chr17:66695039-67221585	Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
2	nsv543411	chr17:66695039-67221585	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
3	nsv908694	chr17:66802992-66913936	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1838100	POLG2	cis	cerebellum	SCAN
rs1838100	LOC440461	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:66826600-66830000	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr17:66826800-66831200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr17:66827000-66830800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr17:66827400-66830200	Enhancers	Adipose Nuclei	Adipose
5	chr17:66828200-66833800	Weak transcription	Fetal Muscle Trunk	muscle
6	chr17:66829000-66831000	Weak transcription	Primary monocytes fromperipheralblood	blood
7	chr17:66829000-66831200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr17:66829200-66830800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr17:66829200-66831000	Weak transcription	Ovary	ovary
10	chr17:66829200-66831400	Weak transcription	Fetal Lung	lung
11	chr17:66829200-66836200	Weak transcription	Fetal Muscle Leg	muscle
12	chr17:66829600-66832400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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