Variant report

Variant	rs13248227
Chromosome Location	chr8:103428008-103428009
allele	G/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	SPI1	chr8:103427963-103428265	HL-60	blood:	n/a	chr8:103428174-103428187

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:103425193..103428090-chr8:103658555..103660884,2	MCF-7	breast:

Variant related genes	Relation type
UBR5	TF binding region
ENSG00000253923	TF binding region

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10109588	0.89[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs12114277	0.87[ASW][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];0.93[LWK][hapmap];0.81[MKK][hapmap];0.87[YRI][hapmap]
rs13266369	0.84[ASN][1000 genomes]
rs13269273	0.83[JPT][hapmap]
rs13270182	0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs13281324	0.96[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2512408	0.86[CHB][hapmap]
rs2512409	0.85[CHD][hapmap];0.84[GIH][hapmap];0.90[LWK][hapmap];0.81[MKK][hapmap];0.86[YRI][hapmap]
rs2607662	0.86[CHD][hapmap];0.87[GIH][hapmap]
rs2607663	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs2853232	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs2853233	0.81[CHD][hapmap];0.84[GIH][hapmap]
rs2853236	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs2853238	0.82[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];0.84[MEX][hapmap]
rs34300781	0.80[ASN][1000 genomes]
rs35065885	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs36027049	0.87[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs4495397	0.95[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4609174	0.89[CHD][hapmap];0.87[JPT][hapmap];0.87[ASN][1000 genomes]
rs4617126	0.91[CHB][hapmap];0.88[YRI][hapmap]
rs4734619	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs4734621	0.81[ASN][1000 genomes]
rs62523127	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6468826	0.91[CHB][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs71209870	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7823262	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7827839	0.93[ASW][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.91[LWK][hapmap];0.90[MKK][hapmap];0.96[YRI][hapmap]
rs7844250	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9642790	0.93[ASN][1000 genomes]
rs9693239	0.87[JPT][hapmap]
rs9694458	0.88[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	nsv1033829	chr8:103110057-103525696	Strong transcription Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv1025935	chr8:103199207-103468322	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv891244	chr8:103309862-103483466	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	nsv831412	chr8:103337196-103536397	Genic enhancers Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
5	esv33118	chr8:103358567-104068172	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
6	nsv1023938	chr8:103369215-103538708	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13248227	PABPC1	cis	cerebellum	SCAN
rs13248227	CTHRC1	cis	parietal	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:103425600-103428600	Weak transcription	Primary neutrophils fromperipheralblood	blood
2	chr8:103425600-103429200	Weak transcription	Right Atrium	heart
3	chr8:103425600-103432600	Weak transcription	Left Ventricle	heart
4	chr8:103425800-103428600	Enhancers	HepG2	liver
5	chr8:103425800-103428800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr8:103425800-103428800	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr8:103425800-103428800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr8:103425800-103429200	Weak transcription	Placenta	Placenta
9	chr8:103425800-103434800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr8:103425800-103437800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr8:103425800-103439600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr8:103425800-103439600	Weak transcription	Fetal Stomach	stomach
13	chr8:103426000-103432200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr8:103426200-103439600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr8:103426400-103428200	Weak transcription	Primary B cells from peripheral blood	blood
16	chr8:103426400-103428600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr8:103426400-103434800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr8:103426600-103428200	Enhancers	GM12878-XiMat	blood
19	chr8:103426600-103429000	Enhancers	K562	blood
20	chr8:103427600-103429400	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr8:103427800-103428200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr8:103427800-103429000	Enhancers	Monocytes-CD14+_RO01746	blood
23	chr8:103427800-103429600	Enhancers	Fetal Intestine Large	intestine
24	chr8:103428000-103429000	Enhancers	Primary B cells from cord blood	blood

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