Variant report

Variant	rs1055429
Chromosome Location	chr3:51570508-51570509
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	CEBPB	chr3:51570186-51570573	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:51563197..51565095-chr3:51570148..51572245,2	K562	blood:
2	chr3:51565204..51566950-chr3:51568740..51571431,2	K562	blood:
3	chr3:51569925..51574030-chr3:51574727..51581311,8	MCF-7	breast:
4	chr3:51566921..51569194-chr3:51569307..51571426,2	MCF-7	breast:

Variant related genes	Relation type
RAD54L2	TF binding region
ENSG00000164080	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1031925	1.00[CEU][hapmap];0.83[CHD][hapmap];0.94[GIH][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes]
rs10865970	0.80[AMR][1000 genomes]
rs11130293	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11719995	0.84[EUR][1000 genomes]
rs11721253	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11917683	1.00[CEU][hapmap]
rs11919197	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];0.84[TSI][hapmap]
rs13090011	0.85[CEU][hapmap]
rs1480353	1.00[CEU][hapmap]
rs1480354	0.80[AMR][1000 genomes]
rs1542574	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap]
rs1552074	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];0.90[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes]
rs17051734	0.85[CHB][hapmap]
rs17051762	0.91[CEU][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap]
rs2127655	0.92[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes]
rs2219890	1.00[CEU][hapmap]
rs3821829	0.85[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap]
rs4067	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.90[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap]
rs4234644	1.00[CEU][hapmap]
rs4317086	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4355273	0.85[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes]
rs4611808	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4687568	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4687569	0.90[AMR][1000 genomes]
rs4687721	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4687734	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4974104	1.00[CEU][hapmap]
rs4974105	0.82[AMR][1000 genomes]
rs4974106	0.80[AMR][1000 genomes]
rs6445628	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes]
rs6445791	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6771081	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6771491	1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes]
rs6775666	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes]
rs6787312	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[GIH][hapmap];0.82[LWK][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6793900	0.92[AMR][1000 genomes]
rs6809155	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7372658	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs751075	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes]
rs7625006	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];0.94[TSI][hapmap]
rs7633708	0.84[CEU][hapmap]
rs9311469	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9866430	0.84[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014464	chr3:51220151-51909780	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs1055429	TEX264	cis	Nerve Tibial	GTEx
rs1055429	NCKIPSD	cis	cerebellum	SCAN
rs1055429	MST1	cis	cerebellum	SCAN
rs1055429	TEX264	cis	Artery Tibial	GTEx
rs1055429	TEX264	cis	Esophagus Muscularis	GTEx
rs1055429	PARP3	cis	parietal	SCAN
rs1055429	IQCF2	cis	parietal	SCAN
rs1055429	TEX264	cis	Stomach	GTEx
rs1055429	HYAL2	cis	parietal	SCAN
rs1055429	HEMK1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51563200-51572000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:51568800-51572000	Enhancers	Placenta	Placenta
3	chr3:51569600-51570600	Enhancers	Osteobl	bone
4	chr3:51569600-51570800	Weak transcription	GM12878-XiMat	blood
5	chr3:51569800-51570600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr3:51569800-51570600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr3:51569800-51570600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr3:51569800-51570600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr3:51569800-51570600	Enhancers	HMEC	breast
10	chr3:51569800-51570600	Enhancers	NHEK	skin
11	chr3:51570000-51571800	Weak transcription	Liver	Liver
12	chr3:51570000-51572000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:51570200-51570600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr3:51570400-51571400	Weak transcription	Placenta Amnion	Placenta Amnion

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