Variant report

Variant	rs4939179
Chromosome Location	chr11:57846710-57846711
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10896705	0.82[LWK][hapmap]
rs11229216	0.86[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs11229225	0.81[AFR][1000 genomes]
rs11229228	0.81[AFR][1000 genomes]
rs11229229	0.81[AFR][1000 genomes]
rs11229232	0.81[AFR][1000 genomes]
rs11229238	0.86[CEU][hapmap];0.91[CHD][hapmap];0.92[TSI][hapmap];0.87[EUR][1000 genomes]
rs11229240	0.86[CEU][hapmap];0.92[CHD][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11229246	0.93[CEU][hapmap];0.93[GIH][hapmap];0.93[LWK][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11229251	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs11229255	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs12793317	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1349481	1.00[YRI][hapmap]
rs1447173	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs17459653	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs17537868	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.82[JPT][hapmap];0.93[LWK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2441956	0.91[CHD][hapmap];0.82[TSI][hapmap]
rs2514205	0.86[CEU][hapmap];0.82[JPT][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28650443	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34216610	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35157521	0.81[AFR][1000 genomes]
rs4938884	0.81[AFR][1000 genomes]
rs4939178	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4939185	0.87[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.91[MEX][hapmap];0.80[TSI][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs61738000	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044030	chr11:57073395-58035564	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
2	nsv541047	chr11:57073395-58035564	Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv1054205	chr11:57544264-58358509	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
4	nsv897589	chr11:57623815-58052357	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv832165	chr11:57806024-58009076	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv523101	chr11:57843506-57871866	Enhancers Weak transcription	TF binding region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4939179	YPEL4	cis	multi-tissue	Pritchard
rs4939179	TIMM10	cis	multi-tissue	Pritchard
rs4939179	TIMM10	cis	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57840800-57847200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr11:57844000-57846800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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