Variant report

Variant	rs10520059
Chromosome Location	chr4:151103731-151103732
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	chr4:151102342..151104330-chr4:151119995..151122046,2	MCF-7	breast:

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10001645	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10001651	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10020361	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10029811	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10033999	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12019295	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12374344	1.00[JPT][hapmap]
rs17026748	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.89[MEX][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];0.85[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2305980	0.86[JPT][hapmap]
rs28361896	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28377256	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28501175	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28598870	0.97[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs28616626	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28635652	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28673979	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4353883	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs59085186	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs60526300	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62338194	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62338212	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62338216	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72732403	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7438777	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9884239	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9884665	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9997755	1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.83[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	nsv1026797	chr4:150246932-151217137	Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv932022	chr4:150831733-151419552	Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1032689	chr4:150971003-151316856	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv537300	chr4:150971003-151316856	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10520059	TIGD4	cis	parietal	SCAN
rs10520059	LRBA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:151091600-151104800	Enhancers	Cortex derived primary cultured neurospheres	brain
2	chr4:151097600-151113800	Weak transcription	Aorta	Aorta
3	chr4:151097600-151129000	Weak transcription	Lung	lung
4	chr4:151098200-151120000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr4:151098200-151128000	Weak transcription	Fetal Stomach	stomach
6	chr4:151100000-151107000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr4:151100000-151127800	Weak transcription	Osteobl	bone
8	chr4:151100200-151116800	Weak transcription	HSMM	muscle
9	chr4:151101000-151104200	Enhancers	Fetal Brain Female	brain
10	chr4:151101200-151104200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
11	chr4:151101400-151104200	Enhancers	Fetal Heart	heart
12	chr4:151101400-151104800	Enhancers	Brain Germinal Matrix	brain
13	chr4:151101600-151104400	Enhancers	Brain Anterior Caudate	brain
14	chr4:151101600-151127600	Weak transcription	Colon Smooth Muscle	Colon
15	chr4:151102000-151104600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr4:151102400-151103800	Enhancers	Brain Hippocampus Middle	brain
17	chr4:151102400-151104000	Enhancers	Brain Cingulate Gyrus	brain
18	chr4:151102400-151104200	Enhancers	Fetal Brain Male	brain
19	chr4:151102800-151105200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr4:151103000-151103800	Enhancers	Adipose Nuclei	Adipose
21	chr4:151103200-151138000	Weak transcription	NH-A	brain
22	chr4:151103400-151104000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr4:151103400-151112200	Weak transcription	Left Ventricle	heart

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