Variant report

Variant	rs12488363
Chromosome Location	chr3:179691697-179691698
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10937015	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13059606	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13059836	0.84[EUR][1000 genomes]
rs13060119	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1522116	0.86[CHB][hapmap];0.83[CHD][hapmap]
rs4855132	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4855133	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4855134	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4855135	1.00[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7647006	1.00[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.92[GIH][hapmap];0.82[JPT][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829807	chr3:179527567-179745153	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv829808	chr3:179574614-179754321	Strong transcription Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv534210	chr3:179666123-179899347	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1000756	chr3:179672703-179827373	Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	esv33044	chr3:179688785-179691941	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12488363	CCDC39	cis	cerebellum	SCAN
rs12488363	CHRD	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:179686400-179691800	Weak transcription	Osteobl	bone
2	chr3:179686800-179692000	Active TSS	Brain Inferior Temporal Lobe	brain
3	chr3:179686800-179692200	Active TSS	Brain Substantia Nigra	brain
4	chr3:179687400-179692200	Active TSS	Brain Anterior Caudate	brain
5	chr3:179688400-179692200	Active TSS	Brain Hippocampus Middle	brain
6	chr3:179688800-179692000	Active TSS	Brain Angular Gyrus	brain
7	chr3:179689400-179710200	Weak transcription	Fetal Brain Male	brain
8	chr3:179690200-179691800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr3:179690200-179692200	Active TSS	Brain Cingulate Gyrus	brain
10	chr3:179690400-179692200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
11	chr3:179690800-179691800	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr3:179690800-179691800	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
13	chr3:179690800-179692200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr3:179690800-179692400	Enhancers	H1 Cell Line	embryonic stem cell
15	chr3:179690800-179692600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr3:179691000-179692000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr3:179691200-179692000	Active TSS	Dnd41	blood
18	chr3:179691400-179692400	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr3:179691400-179692400	Enhancers	iPS-18 Cell Line	embryonic stem cell
20	chr3:179691400-179692600	Enhancers	iPS-15b Cell Line	embryonic stem cell
21	chr3:179691600-179691800	Enhancers	Thymus	Thymus
22	chr3:179691600-179692000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr3:179691600-179692000	Flanking Active TSS	Fetal Thymus	thymus
24	chr3:179691600-179692000	Active TSS	GM12878-XiMat	blood
25	chr3:179691600-179692200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr3:179691600-179692200	Enhancers	iPS-20b Cell Line	embryonic stem cell
27	chr3:179691600-179692200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr3:179691600-179692400	Enhancers	ES-I3 Cell Line	embryonic stem cell
29	chr3:179691600-179692400	Enhancers	HUES64 Cell Line	embryonic stem cell
30	chr3:179691600-179692400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links