Variant report

Variant	rs1546246
Chromosome Location	chr12:117531875-117531876
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10744889	0.96[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10744890	0.96[CEU][hapmap];0.86[CHB][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10774901	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10850754	0.96[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.93[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1106277	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12423796	0.85[ASW][hapmap];0.96[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.94[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1546247	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1546248	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2173651	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4341616	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7304889	0.96[CEU][hapmap];0.83[GIH][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap];0.88[EUR][1000 genomes]
rs7308236	0.96[CEU][hapmap];0.89[CHD][hapmap];0.86[GIH][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7959367	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7963451	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832526	chr12:117530234-117723821	Strong transcription Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1546246	TESC	cis	parietal	SCAN
rs1546246	NCRNA00173	cis	parietal	SCAN
rs1546246	BRAP	cis	parietal	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:117515200-117535200	Weak transcription	Primary T cells from cord blood	blood
2	chr12:117527400-117533200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr12:117528200-117534600	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr12:117528400-117534600	Enhancers	Pancreas	Pancrea
5	chr12:117528800-117536000	Weak transcription	Right Atrium	heart
6	chr12:117529200-117534600	Weak transcription	Brain Anterior Caudate	brain
7	chr12:117529400-117532600	Strong transcription	Primary neutrophils fromperipheralblood	blood
8	chr12:117529400-117534800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr12:117529600-117532400	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr12:117529600-117536000	Weak transcription	Lung	lung
11	chr12:117529800-117532600	Enhancers	Gastric	stomach
12	chr12:117529800-117535000	Weak transcription	Spleen	Spleen
13	chr12:117530000-117534400	Weak transcription	A549	lung
14	chr12:117530000-117535000	Weak transcription	K562	blood
15	chr12:117530200-117535200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr12:117530400-117532400	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr12:117530600-117532000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr12:117531000-117532000	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
19	chr12:117531200-117532200	Enhancers	Right Ventricle	heart
20	chr12:117531200-117532600	Genic enhancers	HepG2	liver
21	chr12:117531400-117532000	Genic enhancers	Stomach Mucosa	stomach
22	chr12:117531400-117532600	Enhancers	Fetal Heart	heart
23	chr12:117531400-117532600	Enhancers	Left Ventricle	heart
24	chr12:117531600-117532000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
25	chr12:117531600-117533200	Weak transcription	Dnd41	blood
26	chr12:117531600-117535000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr12:117531800-117532000	Bivalent Enhancer	Adipose Nuclei	Adipose
28	chr12:117531800-117532000	Enhancers	Fetal Brain Male	brain
29	chr12:117531800-117532000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
30	chr12:117531800-117532400	Enhancers	Fetal Thymus	thymus

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