Variant report

Variant	rs3753460
Chromosome Location	chr1:153322574-153322575
allele	A/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	SPI1	chr1:153322199-153322588	HL-60	blood:	n/a	chr1:153322350-153322363 chr1:153322504-153322517
2	SPI1	chr1:153322103-153322579	HL-60	blood:	n/a	chr1:153322350-153322363 chr1:153322504-153322517
3	SPI1	chr1:153322132-153322788	GM12878	blood:	n/a	chr1:153322350-153322363 chr1:153322504-153322517

No.	Distal block	Cell Line	Cell type
1	chr1:153318291..153319996-chr1:153322460..153325006,2	K562	blood:
2	chr1:153320974..153341807-chr1:153456098..153486349,81	MCF-7	breast:
3	chr1:153314988..153319996-chr1:153321870..153325921,5	K562	blood:

Variant related genes	Relation type
PGLYRP4	TF binding region
ENSG00000263841	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10888551	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.91[ASN][1000 genomes]
rs11589286	0.93[ASN][1000 genomes]
rs12139503	0.87[ASN][1000 genomes]
rs1897695	0.91[ASN][1000 genomes]
rs2117130	0.91[ASN][1000 genomes]
rs2288990	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2916220	0.91[ASN][1000 genomes]
rs2916223	0.93[ASN][1000 genomes]
rs2916224	0.91[ASN][1000 genomes]
rs2916225	0.91[ASN][1000 genomes]
rs2916226	0.91[ASN][1000 genomes]
rs2916227	0.91[ASN][1000 genomes]
rs2916228	0.91[ASN][1000 genomes]
rs2916229	0.91[ASN][1000 genomes]
rs2916230	0.91[ASN][1000 genomes]
rs2916231	0.93[ASN][1000 genomes]
rs2916232	0.91[ASN][1000 genomes]
rs2916233	0.88[ASN][1000 genomes]
rs2916235	0.91[ASN][1000 genomes]
rs2916236	0.91[ASN][1000 genomes]
rs2987759	0.91[ASN][1000 genomes]
rs2987760	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2987763	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2987764	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2987766	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2987767	0.91[ASN][1000 genomes]
rs2987768	0.91[ASN][1000 genomes]
rs2987769	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs3006411	0.91[ASN][1000 genomes]
rs3006427	0.90[ASN][1000 genomes]
rs3006431	0.93[ASN][1000 genomes]
rs3006434	0.93[ASN][1000 genomes]
rs3006439	0.93[ASN][1000 genomes]
rs3006440	0.91[ASN][1000 genomes]
rs3006441	0.91[ASN][1000 genomes]
rs3006444	0.96[ASN][1000 genomes]
rs3006445	0.89[ASN][1000 genomes]
rs3006446	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3006447	0.89[ASN][1000 genomes]
rs3006472	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs3006473	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs3014853	0.91[ASN][1000 genomes]
rs3014854	0.89[ASN][1000 genomes]
rs3014855	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs3014858	0.96[ASN][1000 genomes]
rs3125234	0.89[ASN][1000 genomes]
rs3806230	0.93[ASN][1000 genomes]
rs9435978	0.93[ASN][1000 genomes]
rs9435979	0.90[ASN][1000 genomes]
rs9435983	0.93[ASN][1000 genomes]
rs9436076	0.93[ASN][1000 genomes]
rs9436077	0.93[ASN][1000 genomes]
rs9436084	0.91[ASN][1000 genomes]
rs957195	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9661293	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.91[ASN][1000 genomes]
rs9970937	0.88[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	nsv1010488	chr1:152901263-153670972	Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
2	nsv535171	chr1:152901263-153670972	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
3	nsv533877	chr1:152923645-153468131	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv999024	chr1:153255005-153325685	Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv1002705	chr1:153307852-153525589	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153316200-153330400	Weak transcription	Right Atrium	heart
2	chr1:153317000-153323200	Weak transcription	HMEC	breast
3	chr1:153320400-153322800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr1:153320400-153322800	Enhancers	Esophagus	oesophagus
5	chr1:153321000-153322600	Enhancers	GM12878-XiMat	blood
6	chr1:153321000-153322800	Enhancers	Monocytes-CD14+_RO01746	blood
7	chr1:153321000-153323600	Enhancers	Primary neutrophils fromperipheralblood	blood
8	chr1:153321200-153329400	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr1:153321400-153322600	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr1:153321600-153322600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr1:153321600-153323600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr1:153321800-153322600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr1:153322000-153323600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr1:153322400-153322600	Enhancers	Primary hematopoietic stem cells	blood

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