Variant report

Variant	rs10028144
Chromosome Location	chr4:22691505-22691506
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	CTCF	chr4:22691420-22691570	NB4	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:22684475..22686472-chr4:22689943..22692504,2	K562	blood:
2	chr4:22687079..22688984-chr4:22690023..22692580,2	MCF-7	breast:

Variant related genes	Relation type
GBA3	TF binding region

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10005083	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10030690	0.82[YRI][hapmap]
rs1038112	0.82[ASN][1000 genomes]
rs12498838	0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12506103	0.86[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12508070	0.86[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12509499	0.83[ASN][1000 genomes]
rs12509633	0.97[AFR][1000 genomes]
rs12510458	0.85[ASN][1000 genomes]
rs12510908	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1485826	0.89[YRI][hapmap]
rs1485829	0.86[CHB][hapmap];0.89[CHD][hapmap];0.80[ASN][1000 genomes]
rs1485832	0.85[ASN][1000 genomes]
rs16872987	0.86[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2127178	0.97[AFR][1000 genomes]
rs28374301	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28677984	0.85[ASN][1000 genomes]
rs28727493	0.85[ASN][1000 genomes]
rs3172708	0.86[CHB][hapmap]
rs4146270	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs61793654	0.80[ASN][1000 genomes]
rs6818185	1.00[ASW][hapmap];0.95[LWK][hapmap];0.85[YRI][hapmap];0.97[AFR][1000 genomes]
rs6849406	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7657828	0.86[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7682224	1.00[ASW][hapmap];0.95[LWK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs7684246	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7695833	0.86[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs9884116	0.86[CHB][hapmap];0.84[JPT][hapmap]
rs9884549	0.86[CHB][hapmap];0.86[CHD][hapmap];0.84[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3349061	chr4:22379581-22887563	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv821634	chr4:22427074-22865948	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv829883	chr4:22666326-22842517	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10028144	PI4K2B	cis	cerebellum	SCAN
rs10028144	GPR125	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:22682200-22694600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr4:22682400-22692200	Weak transcription	Liver	Liver
3	chr4:22685200-22693600	Weak transcription	Fetal Intestine Large	intestine
4	chr4:22686200-22692600	Weak transcription	Fetal Intestine Small	intestine
5	chr4:22690800-22692800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
6	chr4:22691000-22691600	Enhancers	Primary hematopoietic stem cells	blood
7	chr4:22691000-22692600	Enhancers	Primary T cells from cord blood	blood

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