Variant report

Variant	rs16845196
Chromosome Location	chr3:115970908-115970909
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10934324	0.84[CHB][hapmap];0.81[CHD][hapmap]
rs10934326	0.83[CEU][hapmap]
rs11920943	0.84[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.86[MEX][hapmap];0.91[MKK][hapmap];0.86[TSI][hapmap];0.87[YRI][hapmap];0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12491423	0.89[CEU][hapmap];0.81[AMR][1000 genomes]
rs12492442	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12495309	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12496133	0.85[CEU][hapmap];0.90[CHB][hapmap]
rs12634800	0.83[CEU][hapmap];0.84[CHB][hapmap]
rs12695324	0.84[CHB][hapmap]
rs13095238	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs1549831	0.83[CEU][hapmap];0.84[CHB][hapmap]
rs16824649	0.83[CEU][hapmap];0.84[CHB][hapmap]
rs16824691	0.81[CEU][hapmap];0.82[CHB][hapmap]
rs16824696	0.83[CEU][hapmap];0.83[CHB][hapmap]
rs1870707	0.83[CEU][hapmap];0.84[CHB][hapmap]
rs1870708	0.81[CEU][hapmap]
rs1870709	0.84[CHB][hapmap];0.81[CHD][hapmap]
rs1993732	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs2279109	0.83[CEU][hapmap];0.84[CHB][hapmap];0.81[CHD][hapmap]
rs3195	0.83[CEU][hapmap];0.84[CHB][hapmap];0.81[JPT][hapmap]
rs4831090	0.83[CEU][hapmap];0.84[CHB][hapmap]
rs4831126	0.84[CHB][hapmap]
rs4831127	0.84[CHB][hapmap]
rs4831128	0.83[CEU][hapmap];0.83[CHB][hapmap]
rs57411025	0.86[AMR][1000 genomes]
rs6438308	0.84[CHB][hapmap];0.81[CHD][hapmap]
rs6778040	0.84[CHB][hapmap];0.81[CHD][hapmap]
rs73140978	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73140979	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73140982	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73143014	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7431707	0.83[CEU][hapmap];0.84[CHB][hapmap]
rs7637684	0.84[CHB][hapmap];0.81[CHD][hapmap]
rs7642172	0.83[CEU][hapmap];0.84[CHB][hapmap];0.81[CHD][hapmap]
rs9830749	0.81[CEU][hapmap];0.84[CHB][hapmap];0.81[CHD][hapmap]
rs9835427	0.83[CEU][hapmap];0.84[CHB][hapmap]
rs9836892	0.83[CEU][hapmap];0.84[CHB][hapmap]
rs9850908	0.81[CEU][hapmap];0.83[CHB][hapmap]
rs9866706	0.84[CHB][hapmap];0.81[CHD][hapmap]

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
rs16845196	STXBP5L	cis	parietal	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:115961000-115971000	Weak transcription	Brain Anterior Caudate	brain
2	chr3:115962400-115983200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:115965800-115983200	Weak transcription	Fetal Brain Male	brain
4	chr3:115967000-115972200	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr3:115968400-115971000	Weak transcription	Fetal Kidney	kidney
6	chr3:115969400-115971200	Enhancers	Rectal Smooth Muscle	rectum
7	chr3:115969800-115971000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr3:115969800-115971200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
9	chr3:115969800-115971600	Enhancers	Brain Inferior Temporal Lobe	brain
10	chr3:115969800-115972400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr3:115969800-115972400	Enhancers	Brain Angular Gyrus	brain
12	chr3:115969800-115973000	Enhancers	Brain Substantia Nigra	brain
13	chr3:115970200-115972400	Enhancers	Fetal Stomach	stomach
14	chr3:115970600-115971200	Enhancers	Fetal Lung	lung
15	chr3:115970600-115971400	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr3:115970600-115972600	Enhancers	HUES64 Cell Line	embryonic stem cell
17	chr3:115970600-115972800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr3:115970600-115973200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr3:115970800-115971400	Enhancers	Brain Cingulate Gyrus	brain
20	chr3:115970800-115971800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr3:115970800-115972000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr3:115970800-115973000	Enhancers	Brain Hippocampus Middle	brain
23	chr3:115970800-115974800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr3:115970800-115976800	Enhancers	Colon Smooth Muscle	Colon

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