Variant report

Variant	rs578057
Chromosome Location	chr11:73996674-73996675
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1279117	0.81[AMR][1000 genomes]
rs1290193	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1783537	0.85[CHB][hapmap];0.81[ASN][1000 genomes]
rs1790398	0.80[CEU][hapmap]
rs1790399	0.80[CEU][hapmap]
rs1941817	0.82[JPT][hapmap]
rs2848559	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4641511	0.83[JPT][hapmap]
rs474280	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs486577	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs490539	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs500608	0.82[CHB][hapmap]
rs513683	0.92[CEU][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs556134	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55660813	0.80[EUR][1000 genomes]
rs627354	0.82[JPT][hapmap];0.80[EUR][1000 genomes]
rs7947390	0.80[EUR][1000 genomes]
rs826056	0.80[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757451	chr11:73842609-74545888	Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	esv2759837	chr11:73842609-74557597	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	esv34979	chr11:73878688-74533452	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
4	esv2758277	chr11:73887567-74557597	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
5	nsv825994	chr11:73936667-74534455	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs578057	P4HA3	cis	Thyroid	GTEx
rs578057	RP11-702H23.4	cis	Thyroid	GTEx

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:73990400-73998800	Weak transcription	HUVEC	blood vessel
2	chr11:73990600-73998800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr11:73990600-73999200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr11:73990600-73999400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr11:73991000-73998800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr11:73992000-73999200	Weak transcription	Aorta	Aorta
7	chr11:73995200-73996800	Weak transcription	Hela-S3	cervix
8	chr11:73995200-73999200	Weak transcription	Colon Smooth Muscle	Colon
9	chr11:73995400-73999000	Weak transcription	NH-A	brain
10	chr11:73995400-73999000	Weak transcription	Osteobl	bone
11	chr11:73995400-73999200	Weak transcription	Stomach Mucosa	stomach
12	chr11:73995600-73998200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr11:73995600-73998800	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr11:73996000-73996800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr11:73996000-73997400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr11:73996000-73998000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr11:73996000-73998600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr11:73996000-73998600	Weak transcription	NHLF	lung
19	chr11:73996000-73998800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr11:73996000-73999000	Weak transcription	HSMM	muscle
21	chr11:73996000-73999200	Weak transcription	NHDF-Ad	bronchial
22	chr11:73996400-73998200	Genic enhancers	A549	lung

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