Variant report

Variant	rs4889009
Chromosome Location	chr16:79700447-79700448
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:79699171..79703517-chr16:79703807..79706802,5	MCF-7	breast:
2	chr16:79698328..79700489-chr16:79701570..79703938,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000221330	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs11150187	0.91[CEU][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11150188	0.81[EUR][1000 genomes]
rs11150190	0.81[EUR][1000 genomes]
rs11644082	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11644758	0.84[CEU][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11644799	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11644836	0.81[EUR][1000 genomes]
rs11645076	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11646791	0.81[EUR][1000 genomes]
rs12149234	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12444166	0.81[EUR][1000 genomes]
rs12449109	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12449161	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1424231	0.91[CEU][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs16950982	0.81[EUR][1000 genomes]
rs16950997	0.92[CEU][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28773265	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4243177	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4490016	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4888043	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4889012	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4889014	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4889015	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56892402	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs59617251	0.81[EUR][1000 genomes]
rs6564688	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7187128	0.85[CEU][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7200841	0.84[CEU][hapmap];0.84[CHB][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7202770	0.92[CEU][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs74037508	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs74037509	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7500666	1.00[CEU][hapmap];0.88[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8047723	0.91[CEU][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8048539	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8048928	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9927134	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][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	nsv573285	chr16:79158182-80127326	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv833295	chr16:79568878-79726768	Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv906992	chr16:79649394-79769790	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv530714	chr16:79661581-79925435	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv833296	chr16:79692236-79889727	Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Thyroid peroxidase antibody positivity	24586183	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4889009	RP11-345M22.2	cis	Skin Sun Exposed Lower leg	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:79697800-79700600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr16:79698600-79703800	Weak transcription	Esophagus	oesophagus
3	chr16:79698600-79703800	Weak transcription	NHEK	skin
4	chr16:79698600-79707000	Weak transcription	Fetal Lung	lung
5	chr16:79698600-79707600	Weak transcription	Ovary	ovary
6	chr16:79698800-79701600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links