Variant report

Variant	rs1713007
Chromosome Location	chr3:116159418-116159419
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1713001	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1731597	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1731598	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1731601	0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1731610	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1795249	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1795263	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1920193	1.00[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2864815	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2902853	0.92[CEU][hapmap];0.81[CHD][hapmap];0.81[MEX][hapmap]
rs3866148	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4626095	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4831140	0.99[EUR][1000 genomes];0.90[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	esv2757886	chr3:116142130-116307542	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	esv2759171	chr3:116142130-116307542	Weak transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1713007	STXBP5L	cis	cerebellum	SCAN
rs1713007	IQCB1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:116143400-116161200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr3:116143600-116161000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr3:116144200-116160400	Weak transcription	Brain Cingulate Gyrus	brain
4	chr3:116144200-116160400	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr3:116152800-116161000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr3:116152800-116161200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr3:116152800-116161400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr3:116153200-116161200	Weak transcription	Colon Smooth Muscle	Colon
9	chr3:116156400-116160400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr3:116158400-116161800	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr3:116158800-116159600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr3:116158800-116159800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr3:116158800-116161600	Enhancers	NH-A	brain
14	chr3:116159000-116160400	Enhancers	Brain Angular Gyrus	brain
15	chr3:116159000-116160400	Enhancers	Brain Hippocampus Middle	brain
16	chr3:116159000-116161000	Enhancers	Brain Substantia Nigra	brain
17	chr3:116159000-116163400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr3:116159200-116159600	Weak transcription	Brain Anterior Caudate	brain
19	chr3:116159200-116160400	Weak transcription	Brain Germinal Matrix	brain
20	chr3:116159200-116161200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr3:116159400-116160400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr3:116159400-116160600	Weak transcription	Rectal Smooth Muscle	rectum
23	chr3:116159400-116161200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr3:116159400-116161200	Weak transcription	HUES64 Cell Line	embryonic stem cell

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