Variant report

Variant	rs16973392
Chromosome Location	chr15:33921082-33921083
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10851886	0.87[CHB][hapmap]
rs11072570	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11853673	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12148690	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12592397	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12593948	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12595559	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs17817434	0.81[TSI][hapmap]
rs28612107	0.81[ASN][1000 genomes]
rs62010505	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62010506	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs937302	0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs951443	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043046	chr15:33714908-34321330	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	esv34037	chr15:33732616-34049083	Enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16973392	APBA2	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:33858000-33921200	Weak transcription	Stomach Smooth Muscle	stomach
2	chr15:33859200-33923200	Weak transcription	Fetal Muscle Trunk	muscle
3	chr15:33873000-33923400	Weak transcription	Brain Anterior Caudate	brain
4	chr15:33891800-33921800	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr15:33895600-33922800	Weak transcription	Aorta	Aorta
6	chr15:33913000-33932200	Weak transcription	Brain Hippocampus Middle	brain
7	chr15:33915000-33959400	Weak transcription	Colon Smooth Muscle	Colon
8	chr15:33915400-33925800	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr15:33915400-33925800	Weak transcription	Rectal Smooth Muscle	rectum
10	chr15:33916400-33922800	Weak transcription	Fetal Muscle Leg	muscle
11	chr15:33918400-33924200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr15:33919400-33923200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr15:33920000-33921200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr15:33920200-33921400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr15:33920200-33927400	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr15:33920400-33931200	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr15:33920800-33923200	Weak transcription	Brain Substantia Nigra	brain
18	chr15:33920800-33931000	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr15:33921000-33923600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr15:33921000-33925600	Weak transcription	Ovary	ovary

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links