Variant report

Variant	rs930799
Chromosome Location	chr18:13319232-13319233
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 68 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10084046	0.86[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs11080642	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11080646	0.86[CHB][hapmap];0.91[CHD][hapmap]
rs11662722	0.83[EUR][1000 genomes]
rs1225	0.83[JPT][hapmap]
rs12456874	0.85[CEU][hapmap]
rs12959004	0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12959077	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12959091	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12961452	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs16940343	0.82[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];0.81[ASN][1000 genomes]
rs16940349	0.95[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1840267	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1869496	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1869497	0.95[CEU][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2085048	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2085049	0.83[JPT][hapmap]
rs2085050	0.94[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2187501	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2187502	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2276392	0.95[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];0.87[JPT][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2867874	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2867875	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2867876	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4570934	0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs4570935	0.94[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4606791	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4797761	0.83[JPT][hapmap]
rs55882226	0.83[EUR][1000 genomes]
rs6505798	0.88[ASW][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];0.82[MEX][hapmap];0.93[MKK][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6505802	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6505803	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7226901	0.95[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7227361	0.90[CEU][hapmap];0.95[CHB][hapmap]
rs7230643	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7231366	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7231701	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7234501	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7234675	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7236152	0.84[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7236934	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7237181	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7237577	0.86[CHB][hapmap];0.93[CHD][hapmap]
rs7241109	0.95[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7241410	0.95[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7241438	0.95[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7242024	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7242140	0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7242207	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7242230	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8087505	0.95[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8088874	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8094197	0.95[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs897035	0.85[CEU][hapmap]
rs9303783	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs930797	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs930798	0.95[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs949259	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs981621	0.86[CHB][hapmap]
rs9946524	0.82[CEU][hapmap];0.82[CHB][hapmap]
rs9952682	0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9952836	0.85[CEU][hapmap];0.86[MEX][hapmap]
rs9953274	0.94[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9954359	0.95[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9957621	0.90[CEU][hapmap]
rs9960893	0.82[AMR][1000 genomes]
rs9963572	0.89[CEU][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531246	chr18:13298774-14082028	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs930799	C18orf19	cis	cerebellum	SCAN
rs930799	ZNF519	cis	parietal	SCAN
rs930799	AFG3L2	cis	cerebellum	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:13314800-13325000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr18:13316600-13322600	Weak transcription	Dnd41	blood
3	chr18:13316800-13320200	Weak transcription	Small Intestine	intestine
4	chr18:13316800-13320600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr18:13317000-13326400	Weak transcription	Brain Angular Gyrus	brain
6	chr18:13317200-13320400	Weak transcription	Fetal Thymus	thymus
7	chr18:13317200-13322000	Weak transcription	Duodenum Mucosa	Duodenum
8	chr18:13317200-13323200	Weak transcription	Brain Germinal Matrix	brain
9	chr18:13317400-13331200	Weak transcription	Primary T cells from cord blood	blood
10	chr18:13318600-13319400	Enhancers	Aorta	Aorta
11	chr18:13318600-13319400	Enhancers	Fetal Muscle Trunk	muscle
12	chr18:13318600-13319400	Enhancers	Left Ventricle	heart
13	chr18:13318600-13319400	Enhancers	Right Atrium	heart
14	chr18:13318600-13319400	Enhancers	Right Ventricle	heart
15	chr18:13318600-13319400	Strong transcription	Thymus	Thymus
16	chr18:13318600-13319600	Enhancers	Fetal Heart	heart
17	chr18:13318600-13319600	Enhancers	Rectal Smooth Muscle	rectum
18	chr18:13318800-13319400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr18:13318800-13319400	Enhancers	Fetal Muscle Leg	muscle
20	chr18:13318800-13319800	Enhancers	Fetal Stomach	stomach
21	chr18:13318800-13319800	Enhancers	Skeletal Muscle Male	skeletal muscle
22	chr18:13318800-13325400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr18:13319000-13319400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr18:13319000-13319400	Enhancers	Stomach Smooth Muscle	stomach
25	chr18:13319000-13319600	Flanking Active TSS	Colon Smooth Muscle	Colon
26	chr18:13319000-13319600	Enhancers	Duodenum Smooth Muscle	Duodenum
27	chr18:13319200-13319400	Enhancers	Brain Anterior Caudate	brain
28	chr18:13319200-13319400	Enhancers	Psoas Muscle	Psoas
29	chr18:13319200-13319400	Enhancers	Spleen	Spleen
30	chr18:13319200-13320200	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr18:13319200-13320400	Enhancers	Liver	Liver
32	chr18:13319200-13321000	Enhancers	Adipose Nuclei	Adipose

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