Variant report

Variant	rs16824696
Chromosome Location	chr3:115984473-115984474
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10934323	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10934324	1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10934326	1.00[CEU][hapmap];0.83[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11719629	0.89[ASN][1000 genomes]
rs11920943	0.83[CHB][hapmap]
rs12492442	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs12494106	0.84[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12496133	0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12634800	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12695324	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13095238	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1381068	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1381070	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1431512	0.88[TSI][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1461121	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1461125	0.93[ASN][1000 genomes]
rs1461126	0.93[ASN][1000 genomes]
rs1544994	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1549831	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1549832	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16824649	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16824686	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16824691	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.84[LWK][hapmap];0.89[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap]
rs16824693	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16845196	0.83[CEU][hapmap];0.83[CHB][hapmap]
rs1870707	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1870708	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1870709	1.00[CHB][hapmap];0.84[CHD][hapmap];0.92[JPT][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1993732	0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2163505	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2279109	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2306064	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2867101	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2867102	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2903483	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3195	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34500521	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4147304	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4831090	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4831126	1.00[CHB][hapmap];0.92[CHD][hapmap];0.92[JPT][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4831127	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4831128	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61254748	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6438308	1.00[CHB][hapmap];0.84[CHD][hapmap];0.92[JPT][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6438310	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6765043	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6778040	1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.93[ASN][1000 genomes]
rs6805045	0.93[ASN][1000 genomes]
rs73141002	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73143006	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73143010	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73861405	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7426468	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7431707	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7624352	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7637684	1.00[CHB][hapmap];0.84[CHD][hapmap];0.92[JPT][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7642172	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7645796	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7653282	0.93[ASN][1000 genomes]
rs9826213	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9828943	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9830749	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9835427	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9836711	0.80[EUR][1000 genomes]
rs9836892	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9850908	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9866532	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9866706	1.00[CHB][hapmap];0.84[CHD][hapmap];0.92[JPT][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9875017	0.82[EUR][1000 genomes];0.93[ASN][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	nsv877360	chr3:115916171-116023990	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
2	esv1808373	chr3:115952799-115984473	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16824696	STXBP5L	cis	parietal	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:115971200-115984800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr3:115976000-115987000	Weak transcription	Brain Anterior Caudate	brain
3	chr3:115976200-115987000	Weak transcription	Brain Angular Gyrus	brain
4	chr3:115979800-115985000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr3:115982000-115987200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr3:115982600-115985600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr3:115982800-115984600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr3:115982800-115985400	Enhancers	Fetal Lung	lung
9	chr3:115983000-115985400	Enhancers	HUES6 Cell Line	embryonic stem cell
10	chr3:115983000-115985600	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr3:115983200-115985200	Enhancers	Brain Germinal Matrix	brain
12	chr3:115983200-115985400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr3:115983200-115985400	Enhancers	Fetal Stomach	stomach
14	chr3:115983200-115986400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr3:115983600-115984600	Enhancers	Brain Substantia Nigra	brain
16	chr3:115983600-115985000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr3:115983600-115985200	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr3:115983600-115985400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr3:115983800-115984800	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
20	chr3:115983800-115985400	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr3:115983800-115985400	Enhancers	Fetal Brain Male	brain
22	chr3:115984000-115984600	Enhancers	Brain Cingulate Gyrus	brain
23	chr3:115984200-115984600	Enhancers	Fetal Brain Female	brain
24	chr3:115984200-115985000	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr3:115984200-115985400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr3:115984400-115984600	Enhancers	Brain Hippocampus Middle	brain
27	chr3:115984400-115984800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr3:115984400-115985400	Enhancers	Colon Smooth Muscle	Colon

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