Variant report

Variant	rs556134
Chromosome Location	chr11:73988410-73988411
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:73982258..73984501-chr11:73987908..73990557,3	K562	blood:
2	chr11:73978845..73982003-chr11:73988326..73991657,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000149380	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10898977	0.83[JPT][hapmap]
rs12365592	0.82[AFR][1000 genomes]
rs1279117	0.82[AMR][1000 genomes]
rs1290193	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1726746	1.00[YRI][hapmap]
rs1783537	0.85[CHB][hapmap];0.81[ASN][1000 genomes]
rs1941817	0.87[JPT][hapmap]
rs2848559	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4641511	0.87[JPT][hapmap]
rs474280	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs474835	1.00[YRI][hapmap]
rs486577	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs490539	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs500608	0.82[CHB][hapmap];1.00[YRI][hapmap]
rs513683	0.92[CEU][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs55660813	0.85[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs578057	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]
rs627354	0.81[CEU][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs642884	0.85[AFR][1000 genomes]
rs7947390	0.81[EUR][1000 genomes]

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
rs556134	RP11-702H23.4	cis	Thyroid	GTEx
rs556134	P4HA3	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:73980200-73989400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr11:73982400-73988800	Weak transcription	Hela-S3	cervix
3	chr11:73985200-73988800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr11:73985200-73989800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr11:73986200-73989600	Weak transcription	HUVEC	blood vessel
6	chr11:73987200-73989000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr11:73987200-73990200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr11:73987200-73990200	Enhancers	Osteobl	bone
9	chr11:73987400-73990200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr11:73987400-73990600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr11:73987400-73990600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr11:73987400-73991000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr11:73987600-73989000	Enhancers	Muscle Satellite Cultured Cells	--
14	chr11:73987600-73989000	Genic enhancers	A549	lung
15	chr11:73987600-73989400	Enhancers	HSMM	muscle
16	chr11:73987600-73990800	Enhancers	NHLF	lung
17	chr11:73987600-73991000	Enhancers	NH-A	brain
18	chr11:73987600-73991000	Enhancers	NHDF-Ad	bronchial
19	chr11:73987800-73989800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr11:73987800-73991000	Enhancers	HSMMtube	muscle
21	chr11:73988200-73988600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr11:73988200-73989800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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