Variant report

Variant	rs301089
Chromosome Location	chr4:53831412-53831413
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:53528226..53530066-chr4:53830131..53832573,2	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10010254	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.94[YRI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11133240	1.00[CEU][hapmap];0.88[CHB][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11726290	0.80[JPT][hapmap]
rs13104612	1.00[CEU][hapmap];0.93[CHB][hapmap];0.85[JPT][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13104971	1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs13120717	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13123449	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13134756	0.89[CHB][hapmap];0.85[GIH][hapmap]
rs1319626	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1384695	1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[GIH][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1531836	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.90[LWK][hapmap];0.89[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2170689	0.96[EUR][1000 genomes]
rs2898683	1.00[CEU][hapmap];0.89[CHB][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs301092	0.85[YRI][hapmap]
rs301110	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs301112	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34704735	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3849652	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs403536	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6554062	0.96[EUR][1000 genomes]
rs6554063	0.93[EUR][1000 genomes]
rs6831230	0.93[EUR][1000 genomes]
rs6844522	0.80[EUR][1000 genomes]
rs6853639	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7685087	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7689426	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs958693	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004889	chr4:53436500-54106281	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv537094	chr4:53436500-54106281	Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv508280	chr4:53825060-53907661	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs301089	TBL1X	trans	brain	seeQTL

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:53786600-53861400	Weak transcription	Primary B cells from cord blood	blood
2	chr4:53808800-53836000	Weak transcription	Esophagus	oesophagus
3	chr4:53816200-53834200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr4:53817200-53832200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr4:53818200-53849800	Weak transcription	Primary T cells from cord blood	blood
6	chr4:53826600-53833400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr4:53827400-53843600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr4:53828200-53833800	Weak transcription	Right Atrium	heart
9	chr4:53829000-53833200	Weak transcription	NHDF-Ad	bronchial
10	chr4:53829000-53842800	Weak transcription	Pancreas	Pancrea
11	chr4:53829400-53832000	Enhancers	Fetal Brain Male	brain
12	chr4:53829800-53831800	Enhancers	Fetal Brain Female	brain
13	chr4:53830400-53832000	Enhancers	Placenta	Placenta
14	chr4:53830800-53832400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr4:53830800-53833000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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