Variant report

Variant	rs473121
Chromosome Location	chr12:121089739-121089740
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:15)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:15 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr12:121089642-121090007	Hela-S3	cervix:	n/a	n/a
2	CEBPB	chr12:121089688-121089978	IMR90	lung:	n/a	n/a
3	USF1	chr12:121089605-121090051	H1-hESC	embryonic stem cell:	n/a	n/a
4	CEBPB	chr12:121089691-121089937	K562	blood:	n/a	n/a
5	MAX	chr12:121089718-121089952	Hela-S3	cervix:	n/a	n/a
6	USF2	chr12:121089682-121090015	Hela-S3	cervix:	n/a	chr12:121089850-121089861
7	MYC	chr12:121089708-121089980	MCF10A-Er-Src	breast:	n/a	n/a
8	CEBPB	chr12:121089693-121089961	A549	lung:	n/a	n/a
9	USF1	chr12:121089592-121090105	HCT-116	colon:	n/a	n/a
10	SPI1	chr12:121089500-121089927	HL-60	blood:	n/a	n/a
11	CEBPB	chr12:121089696-121089973	H1-hESC	embryonic stem cell:	n/a	n/a
12	USF1	chr12:121089625-121089925	A549	lung:	n/a	n/a
13	SPI1	chr12:121089682-121089813	K562	blood:	n/a	n/a
14	MAX	chr12:121089729-121089947	H1-hESC	embryonic stem cell:	n/a	n/a
15	USF1	chr12:121089711-121089933	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

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:

No data

Variant related genes	Relation type
CABP1	TF binding region
ENSG00000256008	Chromatin interaction
ENSG00000157782	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	0.83[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];0.92[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]
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];0.85[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];0.99[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];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs541619	0.87[CHB][hapmap]
rs555379	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]
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
rs473121	UNC119B	cis	parietal	SCAN
rs473121	TAOK3	cis	parietal	SCAN

Chromatin state (count:42 , 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	chr12:121087400-121089800	Active TSS	Left Ventricle	heart
3	chr12:121087600-121090000	Active TSS	Brain Angular Gyrus	brain
4	chr12:121087600-121090200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr12:121087600-121096200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr12:121087800-121093000	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr12:121088000-121089800	Active TSS	Brain Inferior Temporal Lobe	brain
8	chr12:121088200-121090600	Weak transcription	Brain Anterior Caudate	brain
9	chr12:121088200-121092000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr12:121088400-121090600	Weak transcription	GM12878-XiMat	blood
11	chr12:121088600-121090400	Weak transcription	Brain Hippocampus Middle	brain
12	chr12:121088600-121090600	Weak transcription	Right Ventricle	heart
13	chr12:121088800-121090000	Enhancers	Placenta	Placenta
14	chr12:121088800-121090600	Weak transcription	Spleen	Spleen
15	chr12:121089000-121090800	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr12:121089000-121091600	Weak transcription	Rectal Smooth Muscle	rectum
17	chr12:121089000-121092400	Enhancers	Colon Smooth Muscle	Colon
18	chr12:121089200-121090000	Enhancers	A549	lung
19	chr12:121089200-121090200	Enhancers	Right Atrium	heart
20	chr12:121089200-121090200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
21	chr12:121089200-121090400	Enhancers	iPS-15b Cell Line	embryonic stem cell
22	chr12:121089200-121090400	Enhancers	Fetal Stomach	stomach
23	chr12:121089200-121090800	Enhancers	ES-I3 Cell Line	embryonic stem cell
24	chr12:121089400-121089800	Enhancers	H9 Cell Line	embryonic stem cell
25	chr12:121089400-121089800	Enhancers	iPS-20b Cell Line	embryonic stem cell
26	chr12:121089400-121089800	Enhancers	Psoas Muscle	Psoas
27	chr12:121089400-121089800	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
28	chr12:121089400-121090000	Enhancers	H1 Cell Line	embryonic stem cell
29	chr12:121089400-121090000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr12:121089400-121090000	Enhancers	HUES48 Cell Line	embryonic stem cell
31	chr12:121089400-121090800	Enhancers	HUES64 Cell Line	embryonic stem cell
32	chr12:121089400-121091000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
33	chr12:121089600-121089800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
34	chr12:121089600-121089800	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr12:121089600-121089800	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr12:121089600-121089800	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr12:121089600-121089800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr12:121089600-121089800	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr12:121089600-121090000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr12:121089600-121090000	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
41	chr12:121089600-121090000	Bivalent Enhancer	Fetal Muscle Leg	muscle
42	chr12:121089600-121093000	Enhancers	Adipose Nuclei	Adipose

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