Variant report

Variant	rs1003402
Chromosome Location	chr17:15060293-15060294
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs10459907	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1122073	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9896003	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1066329	chr17:14983674-15294071	Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
2	nsv543212	chr17:14983674-15294071	Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
3	nsv574435	chr17:15034841-15060382	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	nsv907701	chr17:15034841-15060382	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
5	nsv907702	chr17:15034841-15065191	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
6	nsv1990	chr17:15041267-15094044	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	nsv492304	chr17:15043353-15611753	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
8	nsv574438	chr17:15043999-15060382	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a
9	nsv457693	chr17:15043999-15060607	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a
10	nsv457694	chr17:15043999-15060607	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a
11	nsv574439	chr17:15043999-15060607	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1003402	FAM18B2	cis	cerebellum	SCAN
rs1003402	SHISA6	cis	parietal	SCAN
rs1003402	TRIM16	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:15058000-15060800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr17:15058000-15061200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr17:15058800-15060800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr17:15058800-15060800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr17:15058800-15061000	Enhancers	NHDF-Ad	bronchial
6	chr17:15059200-15060800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr17:15059400-15060400	Weak transcription	NH-A	brain
8	chr17:15059400-15061000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr17:15059600-15060600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr17:15059600-15061000	Enhancers	Osteobl	bone
11	chr17:15059600-15061200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr17:15059800-15060600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr17:15060000-15060400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr17:15060000-15060800	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr17:15060000-15060800	Enhancers	Monocytes-CD14+_RO01746	blood
16	chr17:15060000-15061000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr17:15060000-15061200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr17:15060200-15060600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr17:15060200-15060800	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
20	chr17:15060200-15061000	Enhancers	ES-WA7 Cell Line	embryonic stem cell

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