Variant report

Variant	rs12906456
Chromosome Location	chr15:49143050-49143051
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:49142203..49145708-chr15:49146118..49148396,4	K562	blood:
2	chr15:49142203..49144495-chr15:49146118..49149143,4	K562	blood:
3	chr15:49101173..49102721-chr15:49142074..49143991,2	K562	blood:

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs12899937	0.85[ASN][1000 genomes]
rs12902606	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.85[ASN][1000 genomes]
rs12909029	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1426199	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[ASN][1000 genomes]
rs17382306	0.85[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.93[MKK][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs17382534	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17383295	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17383671	0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs17466389	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2899424	0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.82[ASN][1000 genomes]
rs34026160	0.85[ASN][1000 genomes]
rs34780506	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs34805202	0.81[ASN][1000 genomes]
rs35706368	0.93[ASN][1000 genomes]
rs35744700	0.85[ASN][1000 genomes]
rs4482220	0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.82[ASN][1000 genomes]
rs56026819	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56287415	0.93[ASN][1000 genomes]
rs62009451	0.84[ASN][1000 genomes]
rs7183535	0.84[CEU][hapmap];0.87[TSI][hapmap];0.85[EUR][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	nsv833001	chr15:49043643-49204765	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12906456	COPS2	cis	parietal	SCAN
rs12906456	FBN1	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49126000-49144800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr15:49127200-49166600	Weak transcription	Brain Cingulate Gyrus	brain
3	chr15:49129400-49147600	Weak transcription	Brain Hippocampus Middle	brain
4	chr15:49129400-49148000	Weak transcription	Brain Angular Gyrus	brain
5	chr15:49131800-49147600	Weak transcription	Right Ventricle	heart
6	chr15:49132200-49150400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr15:49132600-49149000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr15:49133800-49147200	Weak transcription	Fetal Stomach	stomach
9	chr15:49136200-49147800	Weak transcription	Aorta	Aorta
10	chr15:49137000-49147800	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr15:49138200-49144400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
12	chr15:49139000-49147800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr15:49139200-49147800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr15:49140600-49148200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr15:49142200-49147600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr15:49142200-49147600	Weak transcription	Fetal Kidney	kidney
17	chr15:49143000-49143400	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr15:49143000-49143800	Enhancers	Psoas Muscle	Psoas

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