Variant report

Variant	rs1197314
Chromosome Location	chr3:133099245-133099246
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1109858	0.82[JPT][hapmap]
rs1114630	0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1197287	0.86[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs1197288	0.86[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1197293	0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs1197296	0.90[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1197297	0.81[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs1197298	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1197299	0.85[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1197301	0.86[ASN][1000 genomes]
rs1197302	0.86[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1197304	0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.96[ASN][1000 genomes]
rs1197305	0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1197306	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1197308	0.82[JPT][hapmap]
rs1197309	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1197310	0.80[AMR][1000 genomes]
rs1197313	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.85[YRI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1201671	0.86[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1201673	0.81[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs12631678	0.81[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs1619552	0.86[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1619622	0.86[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1708376	0.94[ASN][1000 genomes]
rs1708377	0.86[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1708384	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1708385	0.87[CHB][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs1795101	0.82[JPT][hapmap]
rs1795104	0.90[ASN][1000 genomes]
rs1795107	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2089987	0.83[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs2670179	0.86[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2699880	0.83[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs2699882	0.86[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs3732572	0.81[CEU][hapmap];0.87[CHB][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs4854583	0.89[ASN][1000 genomes]
rs4854719	0.91[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4854720	0.80[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs553211	0.80[AMR][1000 genomes]
rs56181416	0.84[ASN][1000 genomes]
rs656721	0.95[JPT][hapmap]
rs6780144	0.90[ASN][1000 genomes]
rs6802663	0.96[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs938230	0.82[CHD][hapmap]
rs938231	0.83[ASN][1000 genomes]
rs9850193	0.81[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs9853752	0.95[ASN][1000 genomes]
rs9853757	0.95[ASN][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	nsv877503	chr3:133035774-133104631	Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1197314	AMOTL2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:133093000-133102400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:133094000-133099400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr3:133094000-133099800	Weak transcription	HSMMtube	muscle
4	chr3:133094000-133109000	Weak transcription	HSMM	muscle
5	chr3:133094200-133100000	Weak transcription	Brain Hippocampus Middle	brain
6	chr3:133094400-133100000	Weak transcription	Brain Angular Gyrus	brain
7	chr3:133094400-133102800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr3:133094800-133102000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr3:133094800-133110400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr3:133095000-133099600	Weak transcription	Brain Cingulate Gyrus	brain
11	chr3:133095200-133103200	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr3:133095800-133103200	Weak transcription	Fetal Muscle Trunk	muscle
13	chr3:133096000-133107800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr3:133096400-133099800	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr3:133096400-133103200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr3:133097600-133099800	Weak transcription	Fetal Lung	lung
17	chr3:133097600-133100000	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr3:133097800-133102400	Strong transcription	Cortex derived primary cultured neurospheres	brain
19	chr3:133098200-133100000	Strong transcription	Brain Germinal Matrix	brain
20	chr3:133098400-133100000	Strong transcription	Fetal Stomach	stomach
21	chr3:133098400-133100400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr3:133098600-133099800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr3:133098800-133099600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr3:133098800-133099800	Weak transcription	Liver	Liver
25	chr3:133098800-133099800	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr3:133098800-133101400	Enhancers	Pancreas	Pancrea
27	chr3:133098800-133103600	Weak transcription	Spleen	Spleen
28	chr3:133098800-133103800	Enhancers	Fetal Brain Male	brain
29	chr3:133099000-133101600	Genic enhancers	Fetal Brain Female	brain
30	chr3:133099000-133117000	Weak transcription	Placenta	Placenta
31	chr3:133099200-133099600	Strong transcription	Lung	lung
32	chr3:133099200-133099800	Strong transcription	Fetal Muscle Leg	muscle

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