Variant report

Variant	rs12606381
Chromosome Location	chr18:7923843-7923844
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	chr18:7921540..7923960-chr18:7924672..7926506,2	K562	blood:
2	chr18:7919128..7921184-chr18:7922798..7925622,2	K562	blood:

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10502365	0.83[ASW][hapmap];0.90[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11873831	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12606212	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12607648	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1372061	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2120320	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2165412	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28854345	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55742047	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55869040	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56082106	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7227767	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7237870	1.00[CEU][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7244035	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73379961	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8082717	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8087211	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9676009	0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[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
rs12606381	VAPA	cis	parietal	SCAN
rs12606381	TWSG1	cis	parietal	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:7907800-7926600	Weak transcription	Aorta	Aorta
2	chr18:7916000-7924800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr18:7920600-7925000	Enhancers	HMEC	breast
4	chr18:7921800-7924400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr18:7922000-7924000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr18:7922000-7924800	Enhancers	Placenta	Placenta
7	chr18:7922200-7924200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr18:7922200-7924400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr18:7922200-7925000	Weak transcription	Rectal Smooth Muscle	rectum
10	chr18:7922200-7925600	Enhancers	Left Ventricle	heart
11	chr18:7922200-7926600	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr18:7922400-7924200	Enhancers	NHEK	skin
13	chr18:7922400-7925200	Enhancers	HepG2	liver
14	chr18:7922400-7925600	Enhancers	Hela-S3	cervix
15	chr18:7922400-7926000	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr18:7922400-7927200	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr18:7922400-7940600	Weak transcription	Gastric	stomach
18	chr18:7922600-7925200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr18:7922800-7925000	Enhancers	Right Atrium	heart
20	chr18:7923000-7924200	Flanking Active TSS	A549	lung
21	chr18:7923000-7925600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr18:7923000-7936200	Weak transcription	Thymus	Thymus
23	chr18:7923200-7926600	Weak transcription	Stomach Mucosa	stomach
24	chr18:7923400-7924800	Weak transcription	Lung	lung
25	chr18:7923400-7925600	Weak transcription	Psoas Muscle	Psoas
26	chr18:7923400-7926600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr18:7923400-7926600	Weak transcription	Pancreas	Pancrea
28	chr18:7923400-7926600	Weak transcription	NHLF	lung
29	chr18:7923400-7932400	Weak transcription	HSMM	muscle
30	chr18:7923400-7937400	Weak transcription	Right Ventricle	heart
31	chr18:7923400-7945800	Weak transcription	Stomach Smooth Muscle	stomach
32	chr18:7923600-7924000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr18:7923600-7924600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr18:7923600-7924600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr18:7923600-7927200	Weak transcription	Osteobl	bone
36	chr18:7923600-7937000	Weak transcription	Adipose Nuclei	Adipose
37	chr18:7923800-7924800	Weak transcription	Fetal Heart	heart
38	chr18:7923800-7926400	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr18:7923800-7926600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr18:7923800-7926600	Weak transcription	Small Intestine	intestine
41	chr18:7923800-7928200	Weak transcription	Colon Smooth Muscle	Colon
42	chr18:7923800-7936800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links