Variant report

Variant	rs930797
Chromosome Location	chr18:13316513-13316514
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:68)

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];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11080646	0.86[CHB][hapmap];0.91[CHD][hapmap]
rs11662722	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1225	0.83[JPT][hapmap]
rs12456874	0.90[CEU][hapmap];0.80[TSI][hapmap]
rs12959004	0.81[ASN][1000 genomes]
rs12959077	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12959091	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12961452	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16940343	0.81[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs16940349	1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1840267	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1869496	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1869497	1.00[CEU][hapmap];0.98[GIH][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1893980	0.83[CEU][hapmap]
rs2085048	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2085049	0.83[JPT][hapmap]
rs2085050	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2187501	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2187502	0.83[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.90[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2276392	0.90[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];0.87[JPT][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2867874	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2867875	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2867876	0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4570934	0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4570935	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4606791	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4797761	0.83[JPT][hapmap]
rs55882226	0.85[EUR][1000 genomes]
rs6505798	0.86[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs6505802	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6505803	0.95[ASN][1000 genomes]
rs7226901	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7227361	0.95[CEU][hapmap];0.95[CHB][hapmap]
rs7230643	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7231366	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs7231701	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7234501	0.95[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]
rs7234675	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7236152	0.84[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7236934	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7237181	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7237577	0.86[CHB][hapmap];0.93[CHD][hapmap];0.87[LWK][hapmap]
rs7241109	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7241410	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7241438	1.00[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7242024	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7242140	0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7242207	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7242230	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8087505	0.83[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];0.90[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8094197	0.90[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs897035	0.90[CEU][hapmap]
rs9303783	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs930798	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.90[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs930799	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]
rs949259	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs981621	0.86[CHB][hapmap]
rs9946524	0.82[CHB][hapmap]
rs9948620	0.82[MEX][hapmap]
rs9952682	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9952836	0.90[CEU][hapmap];0.90[MEX][hapmap];0.83[TSI][hapmap]
rs9953274	0.95[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9954359	0.90[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9957621	0.95[CEU][hapmap]
rs9960460	0.83[LWK][hapmap]
rs9963572	0.94[CEU][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv2209	chr18:13276410-13316570	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	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
rs930797	AFG3L2	cis	cerebellum	SCAN
rs930797	C18orf19	cis	cerebellum	SCAN
rs930797	TUBB6	cis	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:13303200-13316600	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr18:13303200-13318600	Weak transcription	Rectal Smooth Muscle	rectum
3	chr18:13303200-13318600	Weak transcription	Right Atrium	heart
4	chr18:13303600-13318600	Weak transcription	Colon Smooth Muscle	Colon
5	chr18:13310600-13318600	Weak transcription	Right Ventricle	heart
6	chr18:13314400-13316600	ZNF genes & repeats	Dnd41	blood
7	chr18:13314400-13316800	ZNF genes & repeats	Thymus	Thymus
8	chr18:13314400-13317200	ZNF genes & repeats	Fetal Thymus	thymus
9	chr18:13314600-13317200	ZNF genes & repeats	Brain Germinal Matrix	brain
10	chr18:13314600-13317200	ZNF genes & repeats	Fetal Stomach	stomach
11	chr18:13314800-13325000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr18:13315200-13319200	Weak transcription	Spleen	Spleen
13	chr18:13315800-13316600	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
14	chr18:13315800-13316800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
15	chr18:13315800-13317200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr18:13316000-13317000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
17	chr18:13316200-13316600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr18:13316400-13316800	ZNF genes & repeats	Primary T cells from cord blood	blood
19	chr18:13316400-13316800	ZNF genes & repeats	Left Ventricle	heart
20	chr18:13316400-13318600	Weak transcription	Fetal Heart	heart
21	chr18:13316400-13318600	Weak transcription	Stomach Smooth Muscle	stomach

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