Variant report

Variant	rs1511570
Chromosome Location	chr3:139260828-139260829
allele	C/T
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	chr3:139260820-139260970	HPF	lung:	n/a	chr3:139260934-139260943
2	CTCF	chr3:139260780-139260930	GM12865	blood:	n/a	n/a
3	CTCF	chr3:139260800-139260950	AoAF	blood vessel:	n/a	chr3:139260934-139260943
4	CTCF	chr3:139260800-139260950	GM12868	blood:	n/a	chr3:139260934-139260943
5	CTCF	chr3:139260800-139260950	HVMF	connective:	n/a	chr3:139260934-139260943
6	CTCF	chr3:139260820-139260970	HCFaa	heart:	n/a	chr3:139260934-139260943
7	CTCF	chr3:139260780-139260930	RPTEC	kidney:	n/a	n/a
8	CTCF	chr3:139260820-139260970	K562	blood:	n/a	chr3:139260934-139260943
9	CTCF	chr3:139260820-139260970	HCPEpiC	choroid plexus:	n/a	chr3:139260934-139260943
10	CTCF	chr3:139260800-139261067	H1-hESC	embryonic stem cell:	n/a	chr3:139260934-139260943
11	CTCF	chr3:139260780-139260930	GM06990	blood:	n/a	n/a
12	RAD21	chr3:139260727-139261069	H1-hESC	embryonic stem cell:	n/a	n/a
13	CTCF	chr3:139260820-139260970	HMF	breast:	n/a	chr3:139260934-139260943
14	RAD21	chr3:139260792-139261049	H1-hESC	embryonic stem cell:	n/a	n/a
15	CTCF	chr3:139260800-139260950	HEK293	kidney:	n/a	chr3:139260934-139260943
16	CTCF	chr3:139260820-139260970	GM12867	blood:	n/a	chr3:139260934-139260943
17	CTCF	chr3:139260820-139260970	HVMF	connective:	n/a	chr3:139260934-139260943
18	CTCF	chr3:139260800-139260950	HCT-116	colon:	n/a	chr3:139260934-139260943
19	CTCF	chr3:139260789-139261011	H1-hESC	embryonic stem cell:	n/a	chr3:139260934-139260943
20	CTCF	chr3:139260780-139260930	SAEC	small airway:	n/a	n/a
21	CTCF	chr3:139260780-139260930	HRE	kidney:	n/a	n/a
22	CTCF	chr3:139260820-139260970	GM12873	blood:	n/a	chr3:139260934-139260943
23	KAP1	chr3:139259465-139260908	HEK293	kidney:	n/a	n/a
24	ZNF143	chr3:139260789-139261011	H1-hESC	embryonic stem cell:	n/a	n/a
25	CTCF	chr3:139260820-139260970	HAc	cerebellar:	n/a	chr3:139260934-139260943

No.	Distal block	Cell Line	Cell type
1	chr3:139251954..139254660-chr3:139259598..139262357,2	MCF-7	breast:
2	chr3:139259982..139261816-chr3:139261928..139264277,2	K562	blood:
3	chr3:139260359..139262070-chr3:139266533..139268787,2	MCF-7	breast:
4	chr3:139259820..139261724-chr3:139263779..139266095,2	MCF-7	breast:

Variant related genes	Relation type
RBP1	TF binding region

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1116748	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11549984	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12485273	0.85[CEU][hapmap]
rs12489687	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12493507	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1391029	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1391030	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1391031	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1511571	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17337746	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17397112	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2011770	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3772868	1.00[CEU][hapmap];0.82[YRI][hapmap];0.93[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs3821543	0.92[CEU][hapmap];0.88[YRI][hapmap];0.93[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs4270469	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4407373	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4683502	1.00[CEU][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes]
rs55641400	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55642746	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55724241	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55780517	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55817881	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55834130	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55968289	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55987999	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56034427	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56051054	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56051514	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56058641	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56170893	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56210757	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56343214	0.88[EUR][1000 genomes]
rs57459746	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73220932	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73220940	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73220941	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73220944	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73220945	0.97[ASN][1000 genomes]
rs893703	1.00[CEU][hapmap];1.00[LWK][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs930412	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877543	chr3:139021139-139327261	Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv1003154	chr3:139060841-139788752	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv536729	chr3:139060841-139788752	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	nsv949635	chr3:139091219-139367043	Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv916193	chr3:139187767-139821526	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv530058	chr3:139243971-139814419	Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1511570	RBP1	cis	parietal	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:139259200-139261000	Enhancers	Brain Cingulate Gyrus	brain
2	chr3:139259200-139307000	Weak transcription	Aorta	Aorta
3	chr3:139259400-139261200	Enhancers	Brain Inferior Temporal Lobe	brain
4	chr3:139259600-139261200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr3:139259600-139261200	Enhancers	Right Atrium	heart
6	chr3:139259800-139261600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:139259800-139261800	Enhancers	Fetal Stomach	stomach
8	chr3:139260000-139261000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr3:139260000-139261000	Enhancers	Brain Anterior Caudate	brain
10	chr3:139260000-139261200	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr3:139260000-139261200	Enhancers	Brain Substantia Nigra	brain
12	chr3:139260200-139261200	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
13	chr3:139260200-139261200	Enhancers	Fetal Lung	lung
14	chr3:139260200-139262000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr3:139260400-139261000	Enhancers	Brain Hippocampus Middle	brain
16	chr3:139260600-139261600	Weak transcription	Fetal Kidney	kidney
17	chr3:139260600-139261600	Enhancers	Pancreas	Pancrea
18	chr3:139260600-139262000	Enhancers	Ovary	ovary
19	chr3:139260600-139265600	Weak transcription	Fetal Intestine Small	intestine
20	chr3:139260800-139261000	Enhancers	HMEC	breast
21	chr3:139260800-139261200	Enhancers	Brain Germinal Matrix	brain
22	chr3:139260800-139261400	Enhancers	HUES64 Cell Line	embryonic stem cell
23	chr3:139260800-139261400	Enhancers	Fetal Muscle Trunk	muscle

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