Variant report

Variant	rs555379
Chromosome Location	chr12:121090498-121090499
allele	A/C
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	CTCF	chr12:121090360-121090510	HAc	cerebellar:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:121074234..121078810-chr12:121086912..121091656,5	K562	blood:
2	chr12:121082536..121084918-chr12:121088940..121091677,2	K562	blood:

Variant related genes	Relation type
CABP1	TF binding region
ENSG00000157782	Chromatin interaction
ENSG00000256008	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1168067	0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1168069	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1168070	0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12423417	0.83[ASN][1000 genomes]
rs2461507	0.80[CHD][hapmap];0.87[JPT][hapmap]
rs2673617	1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs2686552	0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2686555	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.99[ASN][1000 genomes]
rs2859263	0.86[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs473121	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4766975	0.88[ASN][1000 genomes]
rs4767921	0.88[ASN][1000 genomes]
rs495265	0.99[ASN][1000 genomes]
rs496212	0.98[ASN][1000 genomes]
rs513175	0.83[CEU][hapmap];0.90[CHB][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs522632	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs526007	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs541619	0.87[CHB][hapmap]
rs568489	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs569499	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.99[ASN][1000 genomes]
rs715120	0.88[ASN][1000 genomes]
rs7305821	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv521928	chr12:121041728-121761800	Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv899557	chr12:121069201-121189116	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1037070	chr12:121069938-121459047	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv1045923	chr12:121082203-121146219	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs555379	TAOK3	cis	parietal	SCAN
rs555379	UNC119B	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121087200-121091000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr12:121087600-121096200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr12:121087800-121093000	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr12:121088200-121090600	Weak transcription	Brain Anterior Caudate	brain
5	chr12:121088200-121092000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr12:121088400-121090600	Weak transcription	GM12878-XiMat	blood
7	chr12:121088600-121090600	Weak transcription	Right Ventricle	heart
8	chr12:121088800-121090600	Weak transcription	Spleen	Spleen
9	chr12:121089000-121090800	Enhancers	HUES6 Cell Line	embryonic stem cell
10	chr12:121089000-121091600	Weak transcription	Rectal Smooth Muscle	rectum
11	chr12:121089000-121092400	Enhancers	Colon Smooth Muscle	Colon
12	chr12:121089200-121090800	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr12:121089400-121090800	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr12:121089400-121091000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr12:121089600-121093000	Enhancers	Adipose Nuclei	Adipose
16	chr12:121089800-121090800	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr12:121089800-121090800	Weak transcription	Psoas Muscle	Psoas
18	chr12:121089800-121090800	Bivalent Enhancer	NHDF-Ad	bronchial
19	chr12:121089800-121091000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr12:121089800-121095400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr12:121090000-121090600	Enhancers	Brain Angular Gyrus	brain
22	chr12:121090000-121091200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
23	chr12:121090000-121092800	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
24	chr12:121090000-121097000	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr12:121090000-121106000	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr12:121090200-121090600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr12:121090200-121091000	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
28	chr12:121090200-121093000	Enhancers	Monocytes-CD14+_RO01746	blood
29	chr12:121090400-121090600	Bivalent Enhancer	Fetal Stomach	stomach
30	chr12:121090400-121090600	Bivalent Enhancer	HSMMtube	muscle
31	chr12:121090400-121090800	Enhancers	Right Atrium	heart
32	chr12:121090400-121091000	Enhancers	H1 Cell Line	embryonic stem cell
33	chr12:121090400-121091000	Bivalent Enhancer	Brain Germinal Matrix	brain
34	chr12:121090400-121091200	Enhancers	Brain Cingulate Gyrus	brain
35	chr12:121090400-121091200	Enhancers	Brain Hippocampus Middle	brain
36	chr12:121090400-121093000	Enhancers	Placenta	Placenta
37	chr12:121090400-121093000	Enhancers	Left Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links