Variant report

Variant	rs10481455
Chromosome Location	chr8:11291341-11291342
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EP300	chr8:11291161-11291400	SK-N-SH_RA	brain:	n/a	n/a
2	GATA2	chr8:11291001-11291935	SH-SY5Y	brain:	n/a	chr8:11291207-11291228 chr8:11291214-11291221 chr8:11291543-11291553 chr8:11291215-11291232 chr8:11291213-11291223 chr8:11291395-11291416 chr8:11291214-11291221 chr8:11291402-11291409 chr8:11291399-11291409 chr8:11291739-11291746 chr8:11291527-11291540 chr8:11291214-11291221
3	GATA3	chr8:11291152-11291589	SH-SY5Y	brain:	n/a	chr8:11291207-11291228 chr8:11291214-11291221 chr8:11291543-11291553 chr8:11291215-11291232 chr8:11291213-11291223 chr8:11291395-11291416 chr8:11291214-11291221 chr8:11291402-11291409 chr8:11291399-11291409 chr8:11291527-11291540 chr8:11291214-11291221
4	REST	chr8:11290997-11291423	SK-N-SH	brain:	n/a	n/a
5	MXI1	chr8:11290628-11292466	SK-N-SH	brain:	n/a	n/a
6	EP300	chr8:11290711-11293404	SK-N-SH	brain:	n/a	chr8:11291721-11291737

Variant related genes	Relation type
C8orf12	TF binding region

Extended variants
information (count: 60 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10088323	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs10102600	0.84[JPT][hapmap];0.90[MEX][hapmap];0.92[AMR][1000 genomes]
rs10448145	0.86[CHB][hapmap];0.82[CHD][hapmap];0.82[ASN][1000 genomes]
rs10503423	0.86[CHB][hapmap]
rs1057750	0.90[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs10903338	0.86[CHB][hapmap];0.83[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs11779875	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs11782375	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs11785710	0.81[ASN][1000 genomes]
rs12114115	0.92[CEU][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.81[TSI][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12543308	0.81[JPT][hapmap]
rs12549796	0.86[CHB][hapmap]
rs12674532	0.90[CHB][hapmap];0.80[CHD][hapmap];0.86[ASN][1000 genomes]
rs13259219	0.90[CHB][hapmap];0.90[JPT][hapmap];0.95[ASN][1000 genomes]
rs13439411	0.86[CHB][hapmap];0.83[CHD][hapmap]
rs2001463	0.95[ASN][1000 genomes]
rs2003423	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs2280803	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2409766	0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2409772	0.81[JPT][hapmap]
rs2409773	0.81[JPT][hapmap]
rs2409775	0.81[JPT][hapmap]
rs2618431	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs2618475	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs2736320	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs28639872	0.95[ASN][1000 genomes]
rs2898279	0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2898280	0.81[JPT][hapmap]
rs4240675	0.91[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4581006	0.85[JPT][hapmap]
rs4840561	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4841529	0.89[JPT][hapmap]
rs4841530	1.00[CEU][hapmap];0.90[CHB][hapmap];0.82[CHD][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4841537	0.81[JPT][hapmap]
rs4841539	0.81[JPT][hapmap]
rs4841540	0.81[CHD][hapmap];0.82[ASN][1000 genomes]
rs6601592	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs6982606	0.92[CEU][hapmap];0.95[CHB][hapmap];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6984212	0.92[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.81[TSI][hapmap];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6998387	0.82[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap]
rs7001675	0.90[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs7003814	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7007712	0.95[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.97[ASN][1000 genomes]
rs7018402	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.84[TSI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7830445	0.81[ASN][1000 genomes]
rs7846252	1.00[CEU][hapmap];0.90[CHB][hapmap];0.82[CHD][hapmap];0.90[MEX][hapmap];0.92[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9693089	0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs9792175	0.81[JPT][hapmap]
rs9792375	0.82[CHB][hapmap];0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1035072	chr8:10819444-11480692	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv539473	chr8:10819444-11480692	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription 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 miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv529399	chr8:10970091-11805960	Enhancers Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	nsv1022525	chr8:11066191-11309356	Enhancers Genic enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv539474	chr8:11066191-11309356	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	esv34097	chr8:11177372-11489894	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	nsv470183	chr8:11236975-11307118	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv465465	chr8:11245064-11307118	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv610275	chr8:11245064-11307118	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv522860	chr8:11253879-11330364	Bivalent/Poised TSS Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS 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
11	nsv890357	chr8:11286146-11330364	Bivalent/Poised TSS Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10481455	CTSB	cis	parietal	SCAN
rs10481455	CTSB	cis	cerebellum	SCAN
rs10481455	TDH	cis	cerebellum	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:11280600-11308800	Weak transcription	Primary B cells from cord blood	blood
2	chr8:11280800-11297600	Weak transcription	Spleen	Spleen
3	chr8:11286000-11295200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr8:11286200-11306400	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr8:11286600-11296200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr8:11287400-11291400	Weak transcription	Left Ventricle	heart
7	chr8:11287400-11296400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr8:11287400-11296400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr8:11287400-11297600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr8:11287600-11291600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr8:11287800-11300600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr8:11287800-11300600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr8:11287800-11313600	Weak transcription	Right Atrium	heart
14	chr8:11288000-11297600	Weak transcription	HSMM	muscle
15	chr8:11288200-11300200	Weak transcription	Brain Hippocampus Middle	brain
16	chr8:11289000-11295400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr8:11289000-11295600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr8:11289600-11291600	Weak transcription	Thymus	Thymus
19	chr8:11289800-11299600	Weak transcription	Brain Anterior Caudate	brain
20	chr8:11289800-11305800	Weak transcription	Osteobl	bone
21	chr8:11290800-11291400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr8:11290800-11293000	Enhancers	Brain Inferior Temporal Lobe	brain
23	chr8:11290800-11293800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr8:11290800-11294000	Enhancers	Fetal Heart	heart
25	chr8:11291000-11291600	Enhancers	Brain Angular Gyrus	brain
26	chr8:11291000-11291800	Strong transcription	NHEK	skin
27	chr8:11291000-11292200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr8:11291000-11292400	Enhancers	Pancreas	Pancrea
29	chr8:11291000-11292600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
30	chr8:11291000-11295000	Enhancers	Fetal Thymus	thymus
31	chr8:11291200-11291400	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
32	chr8:11291200-11291400	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr8:11291200-11291600	Enhancers	Brain Cingulate Gyrus	brain
34	chr8:11291200-11292000	Enhancers	HUES6 Cell Line	embryonic stem cell
35	chr8:11291200-11292200	Enhancers	Stomach Mucosa	stomach
36	chr8:11291200-11292800	Enhancers	Gastric	stomach
37	chr8:11291200-11296200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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