Variant report

Variant	rs4955460
Chromosome Location	chr3:134669241-134669242
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:134667860..134670173-chr3:134674253..134676895,2	K562	blood:

Extended variants
information (count: 53 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs11707505	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs11707539	1.00[JPT][hapmap]
rs11719020	1.00[JPT][hapmap]
rs12495634	1.00[JPT][hapmap]
rs1457560	1.00[JPT][hapmap]
rs1457562	1.00[JPT][hapmap]
rs1457563	1.00[JPT][hapmap]
rs1562508	1.00[JPT][hapmap]
rs1562509	1.00[JPT][hapmap]
rs185257	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs1870196	0.90[CEU][hapmap]
rs1982548	1.00[JPT][hapmap]
rs2045451	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3772657	0.85[CEU][hapmap]
rs3772658	0.81[CEU][hapmap]
rs3940695	1.00[CHB][hapmap];0.82[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4955459	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs4955461	0.85[JPT][hapmap]
rs4955520	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs4955522	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs4955524	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs4955527	1.00[JPT][hapmap]
rs6439537	1.00[JPT][hapmap]
rs6439538	1.00[JPT][hapmap]
rs6768729	1.00[JPT][hapmap]
rs6769854	0.84[CHB][hapmap];0.85[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6776308	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6781640	1.00[JPT][hapmap]
rs6782004	0.80[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6789372	0.86[CEU][hapmap]
rs6795875	1.00[JPT][hapmap]
rs6799875	0.95[CEU][hapmap];0.83[YRI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6801218	0.83[MEX][hapmap]
rs6806959	1.00[JPT][hapmap]
rs7636504	0.84[TSI][hapmap]
rs7644369	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs9289487	1.00[JPT][hapmap]
rs936323	1.00[JPT][hapmap]
rs936324	1.00[JPT][hapmap]
rs936325	0.90[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs972234	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs975148	1.00[CHB][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9815290	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs9818859	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9825380	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs9856814	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs9859282	1.00[JPT][hapmap]
rs9868665	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9869233	1.00[JPT][hapmap]
rs9874260	1.00[ASW][hapmap];0.95[CEU][hapmap];0.82[CHD][hapmap];0.95[GIH][hapmap];0.89[LWK][hapmap];0.88[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]

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	nsv1009634	chr3:134543259-134820208	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv536720	chr3:134543259-134820208	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv1000277	chr3:134546080-134970837	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4955460	EPHB1	cis	lymphoblastoid	seeQTL
rs4955460	EPHB1	cis	multi-tissue	Pritchard

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:134656600-134673000	Weak transcription	GM12878-XiMat	blood
2	chr3:134663800-134669800	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr3:134665000-134676800	Weak transcription	Psoas Muscle	Psoas
4	chr3:134668000-134671000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
5	chr3:134668400-134671400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr3:134669000-134671000	ZNF genes & repeats	Fetal Brain Female	brain
7	chr3:134669200-134670400	ZNF genes & repeats	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr3:134669200-134671000	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
9	chr3:134669200-134671200	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell

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