Variant report

Variant	rs1690684
Chromosome Location	chr10:27944438-27944439
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	chr10:27944057..27945751-chr10:27951830..27953869,2	MCF-7	breast:

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1168571	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1168572	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1168574	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1168582	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1168583	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1168585	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1168586	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1168588	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1168589	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1687722	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1687723	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1687724	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1687730	0.93[EUR][1000 genomes]
rs1687731	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1687732	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1687733	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1687735	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1687736	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1690678	0.89[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs1690685	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1690686	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2253327	1.00[CHD][hapmap]
rs2453213	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2491324	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2505134	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2815539	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv550241	chr10:27569521-28025771	Enhancers ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	esv3368825	chr10:27864181-28043820	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
3	nsv894985	chr10:27869503-27957785	Bivalent Enhancer Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv894986	chr10:27904646-27957785	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1690684	TBL1XR1	trans	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:27933800-27963600	Weak transcription	Ovary	ovary
2	chr10:27941600-27963600	Weak transcription	Stomach Smooth Muscle	stomach
3	chr10:27943800-27944800	Enhancers	Monocytes-CD14+_RO01746	blood
4	chr10:27944200-27944600	Enhancers	NHDF-Ad	bronchial
5	chr10:27944200-27945000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr10:27944400-27947000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr10:27944400-27948600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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