Variant report

Variant	rs1440997
Chromosome Location	chr18:7898534-7898535
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:7)

rs_ID	r²[population]
rs12606453	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12960805	0.81[JPT][hapmap]
rs1866854	0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2165910	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6506539	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9676009	0.86[CEU][hapmap];0.83[EUR][1000 genomes]
rs9961274	0.91[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534374	chr18:7438812-8412546	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv458016	chr18:7488133-7934001	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv576399	chr18:7488133-7934001	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv2762810	chr18:7492090-7924728	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1062911	chr18:7561991-8088274	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv543637	chr18:7561991-8088274	Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv1064345	chr18:7562051-8088274	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv543638	chr18:7562051-8088274	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1440997	TWSG1	cis	parietal	SCAN
rs1440997	VAPA	cis	parietal	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:7857800-7907200	Weak transcription	Thymus	Thymus
2	chr18:7878600-7901400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr18:7886800-7914200	Weak transcription	HepG2	liver
4	chr18:7890000-7905600	Weak transcription	Fetal Thymus	thymus
5	chr18:7890000-7907200	Weak transcription	Lung	lung
6	chr18:7890600-7901800	Weak transcription	Fetal Lung	lung
7	chr18:7890600-7902200	Weak transcription	Fetal Stomach	stomach
8	chr18:7891600-7902400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr18:7895000-7899000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr18:7895200-7898800	Enhancers	Skeletal Muscle Male	skeletal muscle
11	chr18:7896400-7898600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr18:7896400-7898800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr18:7896400-7899200	Enhancers	Right Ventricle	heart
14	chr18:7896400-7900200	Enhancers	Adipose Nuclei	Adipose
15	chr18:7896600-7898800	Enhancers	A549	lung
16	chr18:7896600-7899000	Enhancers	Skeletal Muscle Female	skeletal muscle
17	chr18:7897000-7905400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr18:7897200-7902200	Weak transcription	Hela-S3	cervix
19	chr18:7897400-7898800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr18:7897400-7901400	Weak transcription	Left Ventricle	heart
21	chr18:7897400-7902200	Weak transcription	Colon Smooth Muscle	Colon
22	chr18:7897400-7902200	Weak transcription	Right Atrium	heart
23	chr18:7897400-7913200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr18:7897600-7898800	Weak transcription	Psoas Muscle	Psoas
25	chr18:7897800-7898600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr18:7897800-7902000	Weak transcription	Osteobl	bone
27	chr18:7898000-7902400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr18:7898000-7915200	Weak transcription	Fetal Heart	heart
29	chr18:7898200-7898600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr18:7898200-7898600	Enhancers	Aorta	Aorta
31	chr18:7898200-7898800	Enhancers	Cortex derived primary cultured neurospheres	brain
32	chr18:7898400-7898600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr18:7898400-7898800	Enhancers	H1 Cell Line	embryonic stem cell
34	chr18:7898400-7898800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr18:7898400-7898800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr18:7898400-7898800	Enhancers	HUES6 Cell Line	embryonic stem cell
37	chr18:7898400-7898800	Enhancers	iPS-18 Cell Line	embryonic stem cell
38	chr18:7898400-7899000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr18:7898400-7899000	Enhancers	HUES48 Cell Line	embryonic stem cell
40	chr18:7898400-7899000	Enhancers	HUES64 Cell Line	embryonic stem cell
41	chr18:7898400-7899200	Enhancers	iPS-20b Cell Line	embryonic stem cell

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