Variant report

Variant	rs13046275
Chromosome Location	chr21:40843703-40843704
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	chr21:40843042..40844967-chr21:40948609..40950746,2	MCF-7	breast:
2	chr21:40842346..40845248-chr21:40847999..40850536,2	K562	blood:

Extended variants
information (count: 70 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs11088478	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11701190	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11701232	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11702769	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12482418	0.96[CEU][hapmap];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13050145	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13051411	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1474384	0.96[CEU][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1475593	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1524929	0.96[CEU][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16997763	0.88[YRI][hapmap]
rs16997765	1.00[YRI][hapmap]
rs16997766	0.88[YRI][hapmap]
rs16997767	0.88[YRI][hapmap]
rs2009713	0.85[CEU][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2026268	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2037668	0.96[CEU][hapmap];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2178881	0.99[ASN][1000 genomes]
rs2246616	0.85[CEU][hapmap];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2837043	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2837045	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2837046	0.96[CEU][hapmap];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2837047	0.96[CEU][hapmap];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2837048	0.96[CEU][hapmap];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2837049	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2837050	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2837051	0.82[CEU][hapmap];0.95[ASN][1000 genomes]
rs2837052	0.95[ASN][1000 genomes]
rs2837053	0.96[CEU][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2837054	0.86[CEU][hapmap];0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2837055	0.96[CEU][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28634277	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3787927	0.96[CEU][hapmap];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4118060	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4816629	0.93[ASN][1000 genomes]
rs4818038	0.95[ASN][1000 genomes]
rs4818039	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4818040	0.95[ASN][1000 genomes]
rs4818041	0.96[CEU][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4818042	0.95[ASN][1000 genomes]
rs4818044	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4818045	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4818046	0.86[CEU][hapmap];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6517553	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7277107	0.92[CEU][hapmap];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7277633	0.81[ASN][1000 genomes]
rs7278885	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7280971	1.00[CEU][hapmap];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7281076	0.96[CEU][hapmap];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8126715	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8126729	0.81[CEU][hapmap];0.95[ASN][1000 genomes]
rs8126860	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8127748	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8128567	0.96[CEU][hapmap];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8128795	0.96[CEU][hapmap];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8131355	0.95[ASN][1000 genomes]
rs8132867	0.95[ASN][1000 genomes]
rs8132996	0.81[CEU][hapmap];0.95[ASN][1000 genomes]
rs8133292	0.94[ASN][1000 genomes]
rs8133862	0.95[ASN][1000 genomes]
rs9974333	0.80[CEU][hapmap];0.95[ASN][1000 genomes]
rs9976202	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9976208	0.96[CEU][hapmap];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9983297	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9983428	0.83[CEU][hapmap];0.95[ASN][1000 genomes]
rs9984540	0.96[CEU][hapmap]

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	nsv1059868	chr21:40711535-41043291	Active TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv1061454	chr21:40757973-41265404	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv1062088	chr21:40838027-40919253	Enhancers Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1067330	chr21:40841948-40879552	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs13046275	SH3BGR	cis	Thyroid	GTEx
rs13046275	LCA5L	cis	Muscle Skeletal	GTEx
rs13046275	LCA5L	cis	lung	GTEx
rs13046275	LCA5L	cis	Thyroid	GTEx

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40824000-40852400	Weak transcription	Pancreas	Pancrea
2	chr21:40825000-40847800	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr21:40826600-40849800	Weak transcription	HSMMtube	muscle
4	chr21:40827400-40879800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr21:40828600-40847400	Weak transcription	Brain Substantia Nigra	brain
6	chr21:40828800-40847600	Weak transcription	Brain Angular Gyrus	brain
7	chr21:40828800-40847600	Weak transcription	Brain Anterior Caudate	brain
8	chr21:40829800-40856200	Weak transcription	Aorta	Aorta
9	chr21:40830200-40849800	Weak transcription	Primary T cells from cord blood	blood
10	chr21:40833000-40847200	Weak transcription	Stomach Smooth Muscle	stomach
11	chr21:40835600-40851000	Weak transcription	Ovary	ovary
12	chr21:40835800-40847800	Weak transcription	Left Ventricle	heart
13	chr21:40836200-40851000	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr21:40836200-40852200	Weak transcription	Brain Cingulate Gyrus	brain
15	chr21:40836400-40851400	Weak transcription	Brain Hippocampus Middle	brain
16	chr21:40836400-40894800	Weak transcription	Right Ventricle	heart
17	chr21:40838800-40849800	Weak transcription	Liver	Liver
18	chr21:40840200-40844000	Weak transcription	Fetal Heart	heart
19	chr21:40840600-40844000	Weak transcription	Psoas Muscle	Psoas
20	chr21:40840600-40847600	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr21:40840600-40847800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr21:40840800-40844200	Weak transcription	Skeletal Muscle Female	skeletal muscle

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