Variant report

Variant	rs4798592
Chromosome Location	chr18:7747873-7747874
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:7745866..7749831-chr18:7752461..7755443,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000173482	Chromatin interaction
ENSG00000266767	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10853357	0.96[CEU][hapmap];0.83[JPT][hapmap];0.86[EUR][1000 genomes]
rs11660897	0.87[EUR][1000 genomes]
rs12605941	0.86[EUR][1000 genomes]
rs1446077	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1446078	1.00[CEU][hapmap];0.91[JPT][hapmap];0.86[EUR][1000 genomes]
rs1446085	0.86[EUR][1000 genomes]
rs17556255	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17556324	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1940345	0.86[EUR][1000 genomes]
rs2027670	1.00[CEU][hapmap];0.90[JPT][hapmap];0.86[EUR][1000 genomes]
rs4121621	0.83[CHD][hapmap];0.81[JPT][hapmap]
rs4455047	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs4798582	0.86[EUR][1000 genomes]
rs4798584	0.86[EUR][1000 genomes]
rs4798585	0.86[EUR][1000 genomes]
rs4798587	1.00[CEU][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs4798591	0.86[EUR][1000 genomes]
rs607396	0.83[CHD][hapmap]
rs664592	0.87[CHD][hapmap]
rs680780	0.87[CHD][hapmap]
rs9953589	0.85[CEU][hapmap]
rs9964890	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs9973158	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:25 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064597	chr18:7169490-7762738	Active TSS Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv543636	chr18:7169490-7762738	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised 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	8 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	nsv458017	chr18:7689201-7747873	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv576420	chr18:7689201-7747873	Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	nsv470406	chr18:7700462-7747873	Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
14	nsv1064869	chr18:7730116-7760969	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
15	nsv1061538	chr18:7730116-7762149	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Active TSS Strong transcription	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
16	nsv1067394	chr18:7730116-7768536	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
17	esv2656311	chr18:7732141-7761056	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
18	nsv1057760	chr18:7732188-7760969	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
19	nsv431970	chr18:7732188-7770950	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Strong transcription	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
20	nsv525328	chr18:7732917-7760498	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
21	nsv576421	chr18:7732917-7761056	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
22	nsv576422	chr18:7732917-7763363	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
23	nsv576423	chr18:7732917-7788329	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
24	nsv576424	chr18:7740473-7761056	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
25	nsv576425	chr18:7747873-7859757	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4798592	VAPA	cis	cerebellum	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:7737800-7748400	Weak transcription	Gastric	stomach
2	chr18:7739000-7750600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr18:7742000-7748200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr18:7742000-7751400	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr18:7742800-7748400	Weak transcription	Fetal Stomach	stomach
6	chr18:7744200-7749000	Weak transcription	Brain Anterior Caudate	brain
7	chr18:7745600-7748000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr18:7745600-7748200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr18:7745600-7750800	Weak transcription	Aorta	Aorta
10	chr18:7746200-7748200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr18:7746200-7748200	Weak transcription	Fetal Kidney	kidney
12	chr18:7746200-7748400	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr18:7746600-7748000	Enhancers	Fetal Thymus	thymus
14	chr18:7746600-7750000	Enhancers	Left Ventricle	heart
15	chr18:7746600-7750000	Enhancers	Psoas Muscle	Psoas
16	chr18:7746600-7750000	Enhancers	Right Atrium	heart
17	chr18:7746800-7748000	Enhancers	Thymus	Thymus
18	chr18:7746800-7748200	Enhancers	Adipose Nuclei	Adipose
19	chr18:7746800-7748200	Enhancers	Skeletal Muscle Female	skeletal muscle
20	chr18:7746800-7748400	Weak transcription	A549	lung
21	chr18:7746800-7749800	Enhancers	Lung	lung
22	chr18:7746800-7749800	Enhancers	Spleen	Spleen
23	chr18:7746800-7751400	Enhancers	Right Ventricle	heart
24	chr18:7746800-7752000	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr18:7746800-7753600	Enhancers	HepG2	liver
26	chr18:7747000-7752000	Enhancers	Fetal Heart	heart
27	chr18:7747200-7750200	Enhancers	Colon Smooth Muscle	Colon
28	chr18:7747400-7748200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr18:7747400-7748200	Weak transcription	Pancreas	Pancrea
30	chr18:7747400-7748200	Enhancers	Small Intestine	intestine
31	chr18:7747400-7749000	Weak transcription	Fetal Intestine Large	intestine
32	chr18:7747600-7748000	Weak transcription	Rectal Smooth Muscle	rectum
33	chr18:7747600-7748200	Weak transcription	Osteobl	bone
34	chr18:7747600-7749000	Weak transcription	Fetal Intestine Small	intestine
35	chr18:7747600-7750000	Enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr18:7747800-7748800	Enhancers	Stomach Smooth Muscle	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links