Variant report

Variant	rs4317549
Chromosome Location	chr8:125392860-125392861
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:125383456..125386526-chr8:125392449..125395864,3	MCF-7	breast:
2	chr8:125191744..125194449-chr8:125391340..125393349,2	MCF-7	breast:
3	chr8:125278138..125281039-chr8:125391343..125392943,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164983	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10110968	0.87[LWK][hapmap];0.81[MKK][hapmap];0.86[EUR][1000 genomes]
rs10464864	0.83[GIH][hapmap];0.92[MKK][hapmap];0.80[EUR][1000 genomes]
rs12674575	1.00[GIH][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap]
rs12674701	0.85[EUR][1000 genomes]
rs4257990	0.86[EUR][1000 genomes]
rs4314633	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4506195	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4527851	0.93[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4581036	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4590425	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4639495	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4871489	0.93[CEU][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap]
rs6470241	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6984232	0.86[EUR][1000 genomes]
rs6985308	1.00[GIH][hapmap];0.93[LWK][hapmap];0.89[MEX][hapmap];0.92[MKK][hapmap];0.88[EUR][1000 genomes]
rs6993858	0.88[EUR][1000 genomes]
rs6997326	0.90[MKK][hapmap]
rs7002456	1.00[GIH][hapmap];0.94[LWK][hapmap];0.89[MEX][hapmap];0.95[MKK][hapmap];0.86[EUR][1000 genomes]
rs7010910	0.86[EUR][1000 genomes]
rs7386298	0.88[EUR][1000 genomes]
rs7387520	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7819902	0.86[EUR][1000 genomes]
rs7835851	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7841552	0.87[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	esv2762769	chr8:125167256-125480574	Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv521356	chr8:125309055-125404763	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv1034768	chr8:125323011-125481733	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv527751	chr8:125338216-125431030	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
5	nsv531508	chr8:125390194-125587953	Flanking Active TSS Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4317549	TRMT12	cis	parietal	SCAN

Chromatin state (count:0 , 50 per page) page:

No data

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