Variant report

Variant	rs13298062
Chromosome Location	chr9:13941513-13941514
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10810058	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10961339	1.00[JPT][hapmap]
rs13283645	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13283743	1.00[JPT][hapmap]
rs13285663	0.93[ASN][1000 genomes]
rs13286204	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13291088	0.92[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs13292270	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13292571	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13299074	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13299961	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17192194	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17277467	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17277593	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17278798	1.00[JPT][hapmap]
rs34602246	0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs34660040	0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs34764349	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35165583	0.92[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs35246532	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35249758	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35377705	0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs35684545	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35727886	0.92[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs35907479	0.92[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs35911657	0.92[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs35960404	0.92[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs55776100	0.81[ASN][1000 genomes]
rs7023574	1.00[JPT][hapmap]
rs71511071	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71511072	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022001	chr9:13717736-13983738	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1033764	chr9:13764918-14226168	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv613635	chr9:13893246-13961462	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv1015319	chr9:13931836-13970419	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
5	nsv613636	chr9:13936438-13975480	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13298062	SNAPC3	cis	parietal	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:13933600-13961600	Weak transcription	Psoas Muscle	Psoas
2	chr9:13936200-13942000	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr9:13938000-13943000	Enhancers	Fetal Lung	lung
4	chr9:13938400-13948000	Weak transcription	Right Ventricle	heart
5	chr9:13938600-13942000	Enhancers	Muscle Satellite Cultured Cells	--
6	chr9:13939600-13944000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr9:13939600-13944200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr9:13939800-13941800	Weak transcription	Fetal Stomach	stomach
9	chr9:13939800-13942200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr9:13939800-13942200	Weak transcription	NHEK	skin
11	chr9:13939800-13956200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr9:13940000-13941800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr9:13940000-13941800	Weak transcription	NH-A	brain
14	chr9:13940000-13942000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr9:13940000-13942200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr9:13940000-13942200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr9:13940000-13942200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr9:13940000-13942200	Weak transcription	Hela-S3	cervix
19	chr9:13940000-13942200	Weak transcription	NHLF	lung
20	chr9:13940000-13942800	Weak transcription	Aorta	Aorta
21	chr9:13940200-13942200	Weak transcription	HUVEC	blood vessel
22	chr9:13940400-13962000	Weak transcription	Left Ventricle	heart
23	chr9:13940600-13943400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr9:13940800-13941600	Weak transcription	Ovary	ovary
25	chr9:13940800-13941800	Weak transcription	Fetal Muscle Leg	muscle
26	chr9:13940800-13941800	Weak transcription	HMEC	breast
27	chr9:13940800-13942200	Weak transcription	Osteobl	bone
28	chr9:13941000-13941800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr9:13941000-13942800	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr9:13941000-13943400	Enhancers	HSMM	muscle
31	chr9:13941200-13943400	Enhancers	NHDF-Ad	bronchial
32	chr9:13941400-13942400	Enhancers	HSMMtube	muscle
33	chr9:13941400-13942600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

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