Variant report

Variant	rs2958089
Chromosome Location	chr3:111001016-111001017
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:110999834..111001841-chr3:111004856..111006782,2	MCF-7	breast:

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1303794	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13065090	0.85[EUR][1000 genomes]
rs13085579	0.82[EUR][1000 genomes]
rs13100130	1.00[EUR][1000 genomes]
rs1387223	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1387224	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2087336	0.94[EUR][1000 genomes]
rs2675578	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2698325	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2932066	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2932067	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2958069	0.94[EUR][1000 genomes]
rs2958090	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2971348	0.94[EUR][1000 genomes]
rs2971356	0.94[EUR][1000 genomes]
rs35218644	0.94[EUR][1000 genomes]
rs35327087	0.85[EUR][1000 genomes]
rs35380390	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35791065	0.85[EUR][1000 genomes]
rs36019095	0.94[EUR][1000 genomes]
rs36126940	0.88[EUR][1000 genomes]
rs36128965	0.88[EUR][1000 genomes]
rs61333742	1.00[EUR][1000 genomes]
rs6767554	0.94[EUR][1000 genomes]
rs71315871	0.94[EUR][1000 genomes]
rs71315872	0.94[EUR][1000 genomes]
rs7611652	0.94[EUR][1000 genomes]
rs7622049	0.85[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	nsv1003106	chr3:110264476-111105943	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv460821	chr3:110637471-111501097	Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv591275	chr3:110637471-111501097	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv829675	chr3:110885605-111101858	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv877339	chr3:110889974-111070554	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2958089	TK2	trans	brain	seeQTL

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:110996400-111003400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr3:110996800-111001200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr3:110997000-111003800	Weak transcription	Thymus	Thymus
4	chr3:110997400-111003000	Weak transcription	Primary T cells from cord blood	blood
5	chr3:110997800-111003400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr3:110998600-111004200	Weak transcription	HSMMtube	muscle
7	chr3:110999600-111002200	Enhancers	Fetal Thymus	thymus
8	chr3:111000400-111003400	Enhancers	Dnd41	blood
9	chr3:111000600-111001200	Active TSS	Pancreatic Islets	Pancreatic Islet
10	chr3:111001000-111003000	Weak transcription	Primary T helper cells PMA-I stimulated	--

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