Variant report

Variant	rs9315701
Chromosome Location	chr13:40117992-40117993
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10047779	0.83[AMR][1000 genomes]
rs1885759	0.96[CEU][hapmap];0.84[JPT][hapmap];0.91[EUR][1000 genomes]
rs2324337	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35396912	0.88[EUR][1000 genomes]
rs7322336	0.96[CEU][hapmap];0.84[JPT][hapmap];0.91[EUR][1000 genomes]
rs7333056	0.96[CEU][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs7981547	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7982917	0.96[CEU][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7996238	0.83[GIH][hapmap]
rs9315700	0.83[AMR][1000 genomes]
rs9315702	1.00[CEU][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9315703	0.96[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9315706	0.96[CEU][hapmap];0.84[JPT][hapmap];0.91[EUR][1000 genomes]
rs9315707	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs9532396	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9532399	0.91[EUR][1000 genomes]
rs9548804	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9548805	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9548809	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9548817	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9548819	0.96[CEU][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9548820	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9548821	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9548822	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9548824	0.91[EUR][1000 genomes]
rs9548825	0.96[CEU][hapmap];0.84[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs9548826	0.96[CEU][hapmap];0.84[JPT][hapmap];0.91[EUR][1000 genomes]
rs9548827	0.84[JPT][hapmap];0.91[EUR][1000 genomes]
rs9548829	0.96[CEU][hapmap];0.84[JPT][hapmap];0.91[EUR][1000 genomes]
rs9548830	0.96[CEU][hapmap]
rs9576848	0.85[JPT][hapmap]
rs9603564	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2754118	chr13:39347702-40222644	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1054600	chr13:39801283-40545027	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
3	nsv1050137	chr13:40090742-40118499	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats	lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9315701	FOXO1	cis	parietal	SCAN
rs9315701	ELF1	cis	parietal	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:40106800-40124000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr13:40107800-40140200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr13:40111200-40133200	Weak transcription	Aorta	Aorta
4	chr13:40111400-40128200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr13:40111600-40120600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr13:40111600-40128600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr13:40112000-40122400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr13:40113800-40128600	Weak transcription	Ovary	ovary
9	chr13:40114000-40131200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr13:40114200-40125200	Weak transcription	HSMM	muscle
11	chr13:40114400-40136000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr13:40115400-40133200	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr13:40115600-40120800	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr13:40115600-40133600	Weak transcription	Osteobl	bone
15	chr13:40115800-40120600	Weak transcription	Left Ventricle	heart
16	chr13:40117000-40119600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr13:40117000-40130000	Weak transcription	Fetal Muscle Leg	muscle
18	chr13:40117000-40130400	Weak transcription	HSMMtube	muscle
19	chr13:40117200-40119200	Enhancers	Fetal Heart	heart
20	chr13:40117400-40118000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr13:40117600-40118200	Enhancers	NHEK	skin
22	chr13:40117600-40126400	Weak transcription	Right Ventricle	heart
23	chr13:40117800-40120000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr13:40117800-40128600	Weak transcription	Right Atrium	heart
25	chr13:40117800-40131200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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