Variant report

Variant	rs58139259
Chromosome Location	chr8:104913430-104913431
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10104167	0.94[ASN][1000 genomes]
rs10453058	0.91[ASN][1000 genomes]
rs10505052	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10955332	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10955333	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10955334	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12155936	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12156016	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12156323	1.00[ASN][1000 genomes]
rs12335221	0.94[ASN][1000 genomes]
rs12542692	1.00[ASN][1000 genomes]
rs12548406	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12549891	0.83[EUR][1000 genomes]
rs12550348	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12675494	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12682214	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs16870788	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16870792	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17238250	1.00[ASN][1000 genomes]
rs17238501	1.00[ASN][1000 genomes]
rs17239114	0.94[ASN][1000 genomes]
rs1954898	0.91[ASN][1000 genomes]
rs1954899	0.91[ASN][1000 genomes]
rs2023025	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2023026	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2023028	1.00[ASN][1000 genomes]
rs2023030	0.97[ASN][1000 genomes]
rs2023034	0.94[ASN][1000 genomes]
rs2096978	0.89[ASN][1000 genomes]
rs2132644	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2173081	0.87[AMR][1000 genomes]
rs28826404	0.94[ASN][1000 genomes]
rs28873475	1.00[ASN][1000 genomes]
rs4446700	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4734085	0.91[ASN][1000 genomes]
rs4734738	0.97[ASN][1000 genomes]
rs56123555	1.00[ASN][1000 genomes]
rs56232122	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56369021	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs58345884	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61229244	1.00[ASN][1000 genomes]
rs7009080	0.94[ASN][1000 genomes]
rs7357464	0.94[ASN][1000 genomes]
rs73699009	1.00[ASN][1000 genomes]
rs73699011	1.00[ASN][1000 genomes]
rs7841847	0.97[ASN][1000 genomes]
rs7844763	0.94[ASN][1000 genomes]
rs9650010	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9650011	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9802039	1.00[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	nsv1020476	chr8:104312212-104924482	Genic enhancers Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv539704	chr8:104312212-104924482	Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	esv2752692	chr8:104520824-105123824	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv1016387	chr8:104578389-104931853	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1031195	chr8:104601231-105194208	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
6	nsv831415	chr8:104907757-105115320	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs58139259	RP11-1C8.7	cis	Thyroid	GTEx
rs58139259	RIMS2	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:104897200-104914200	Weak transcription	HUES48 Cell Line	embryonic stem cell
2	chr8:104898200-104919000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr8:104899400-104933400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr8:104913200-104914600	Enhancers	Fetal Intestine Large	intestine
5	chr8:104913200-104914600	Enhancers	Fetal Intestine Small	intestine
6	chr8:104913400-104914400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links