Variant report

Variant	rs4754780
Chromosome Location	chr11:101450781-101450782
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10219300	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10219398	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10791504	0.82[TSI][hapmap]
rs10895138	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10895139	0.94[CEU][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10895144	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10895148	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10895160	0.87[EUR][1000 genomes]
rs11224830	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11224875	1.00[CEU][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11523959	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12280648	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12282925	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1892873	0.89[EUR][1000 genomes]
rs1938830	0.88[EUR][1000 genomes]
rs1938840	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1939449	0.88[EUR][1000 genomes]
rs1939451	0.88[EUR][1000 genomes]
rs1939452	0.88[EUR][1000 genomes]
rs2105612	0.88[EUR][1000 genomes]
rs2154992	0.85[EUR][1000 genomes]
rs2154996	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2154997	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2186577	0.86[EUR][1000 genomes]
rs2186578	0.88[EUR][1000 genomes]
rs2226558	0.87[EUR][1000 genomes]
rs2508244	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2508246	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2508250	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2508251	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2508252	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2508254	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2508725	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2508726	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2508727	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2508728	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2508729	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2513191	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3018705	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3018706	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3018707	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs41302375	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4754778	1.00[CEU][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56134796	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6590893	0.86[EUR][1000 genomes]
rs6590894	0.83[EUR][1000 genomes]
rs7107018	0.87[EUR][1000 genomes]
rs7107512	0.88[EUR][1000 genomes]
rs7112189	0.85[EUR][1000 genomes]
rs7116889	0.88[EUR][1000 genomes]
rs7119712	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7119886	0.82[EUR][1000 genomes]
rs7125321	0.96[EUR][1000 genomes]
rs7126770	0.86[EUR][1000 genomes]
rs7942189	0.99[EUR][1000 genomes]
rs9326314	0.82[TSI][hapmap]
rs947992	0.95[EUR][1000 genomes]
rs9988861	0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv556131	chr11:100985777-101480017	Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
2	nsv530644	chr11:101010088-101486038	Strong transcription Weak transcription Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
3	nsv898330	chr11:101243644-101722031	Enhancers Bivalent/Poised TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
4	esv2754308	chr11:101409790-101502790	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv898331	chr11:101436689-101492630	Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv1052159	chr11:101439655-101853293	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv1051457	chr11:101446705-101837650	Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4754780	TPBG	trans	lymphoblastoid	seeQTL

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:101446800-101452800	Weak transcription	Ovary	ovary
2	chr11:101447800-101452400	Weak transcription	Colon Smooth Muscle	Colon
3	chr11:101448600-101452400	Weak transcription	NHLF	lung
4	chr11:101450200-101451000	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
5	chr11:101450600-101450800	Weak transcription	NHDF-Ad	bronchial
6	chr11:101450600-101451800	Enhancers	Breast Myoepithelial Primary Cells	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links