Variant report

Variant	rs2026268
Chromosome Location	chr21:40856397-40856398
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr21:40855754-40856525	SK-N-SH	brain:	n/a	chr21:40856430-40856437 chr21:40855985-40855992 chr21:40856423-40856444 chr21:40855983-40855993 chr21:40856148-40856155 chr21:40856426-40856442 chr21:40855985-40855992 chr21:40856148-40856155 chr21:40856430-40856437 chr21:40856117-40856126 chr21:40855978-40855999 chr21:40856430-40856437 chr21:40855981-40855994 chr21:40855985-40855992 chr21:40856148-40856155 chr21:40855983-40855992
2	JUND	chr21:40855884-40856406	MCF-7	breast:	n/a	n/a
3	GATA3	chr21:40855766-40856511	MCF-7	breast:	n/a	chr21:40856430-40856437 chr21:40855985-40855992 chr21:40856423-40856444 chr21:40855983-40855993 chr21:40856148-40856155 chr21:40856426-40856442 chr21:40855985-40855992 chr21:40856148-40856155 chr21:40856430-40856437 chr21:40856117-40856126 chr21:40855978-40855999 chr21:40856430-40856437 chr21:40855981-40855994 chr21:40855985-40855992 chr21:40856148-40856155 chr21:40855983-40855992
4	GATA3	chr21:40855695-40856557	SK-N-SH	brain:	n/a	chr21:40856430-40856437 chr21:40855985-40855992 chr21:40856423-40856444 chr21:40855983-40855993 chr21:40856148-40856155 chr21:40856426-40856442 chr21:40855985-40855992 chr21:40856148-40856155 chr21:40856430-40856437 chr21:40856117-40856126 chr21:40855978-40855999 chr21:40856430-40856437 chr21:40855981-40855994 chr21:40855985-40855992 chr21:40856148-40856155 chr21:40855983-40855992
5	GATA1	chr21:40854994-40856502	K562	blood:	n/a	chr21:40856430-40856437 chr21:40855985-40855992 chr21:40856423-40856444 chr21:40855983-40855993 chr21:40856148-40856155 chr21:40856426-40856442 chr21:40855985-40855992 chr21:40856148-40856155 chr21:40856430-40856437 chr21:40856117-40856126 chr21:40855978-40855999 chr21:40856430-40856437 chr21:40855981-40855994 chr21:40855985-40855992 chr21:40856148-40856155 chr21:40855983-40855992
6	GATA3	chr21:40855858-40856510	MCF-7	breast:	n/a	chr21:40856430-40856437 chr21:40855985-40855992 chr21:40856423-40856444 chr21:40855983-40855993 chr21:40856148-40856155 chr21:40856426-40856442 chr21:40855985-40855992 chr21:40856148-40856155 chr21:40856430-40856437 chr21:40856117-40856126 chr21:40855978-40855999 chr21:40856430-40856437 chr21:40855981-40855994 chr21:40855985-40855992 chr21:40856148-40856155 chr21:40855983-40855992
7	JUN	chr21:40855239-40857117	K562	blood:	n/a	chr21:40855430-40855442 chr21:40855475-40855487
8	JUND	chr21:40855802-40856403	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr21:40855062..40856739-chr21:40872543..40874201,2	K562	blood:
2	chr21:40854953..40857406-chr21:40860627..40862371,2	MCF-7	breast:
3	chr21:40825465..40827848-chr21:40854649..40856447,2	K562	blood:

Variant related genes	Relation type
MYL6P2	TF binding region

Extended variants
information (count: 66 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs11088478	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11701190	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11701232	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11702769	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12482418	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13046275	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13050145	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13051411	0.93[ASN][1000 genomes]
rs1474384	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1475593	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1524929	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2009713	0.97[ASN][1000 genomes]
rs2037668	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2178881	0.96[ASN][1000 genomes]
rs2246616	0.96[ASN][1000 genomes]
rs2837043	0.97[ASN][1000 genomes]
rs2837045	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2837046	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2837047	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2837048	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2837049	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2837050	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2837051	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2837052	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2837053	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2837054	0.97[ASN][1000 genomes]
rs2837055	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28634277	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28728311	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3787927	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4118060	0.97[ASN][1000 genomes]
rs4816629	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4818038	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4818039	0.95[ASN][1000 genomes]
rs4818040	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4818041	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4818042	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4818044	0.96[ASN][1000 genomes]
rs4818045	0.95[ASN][1000 genomes]
rs4818046	0.95[ASN][1000 genomes]
rs6517553	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7277107	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7278885	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7280971	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7281076	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8126715	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8126729	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8126860	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8127748	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8128567	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8128795	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8131355	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8132867	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8132996	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8133292	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8133862	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9974333	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9976202	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9976208	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9983297	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9983428	0.81[AMR][1000 genomes];0.97[ASN][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	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
5	esv2755103	chr21:40847196-40877805	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2026268	LCA5L	cis	lung	GTEx
rs2026268	LCA5L	cis	Muscle Skeletal	GTEx
rs2026268	SH3BGR	cis	Thyroid	GTEx
rs2026268	LCA5L	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40827400-40879800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr21:40836400-40894800	Weak transcription	Right Ventricle	heart
3	chr21:40845000-40856600	Weak transcription	Colon Smooth Muscle	Colon
4	chr21:40846800-40862800	Weak transcription	Gastric	stomach
5	chr21:40848200-40895600	Weak transcription	Stomach Smooth Muscle	stomach
6	chr21:40848400-40863600	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr21:40848400-40872400	Weak transcription	Left Ventricle	heart
8	chr21:40850400-40859200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr21:40852600-40863400	Weak transcription	Brain Cingulate Gyrus	brain
10	chr21:40853000-40862200	Weak transcription	Brain Anterior Caudate	brain
11	chr21:40853000-40865800	Weak transcription	Brain Hippocampus Middle	brain
12	chr21:40853800-40857000	Enhancers	Skeletal Muscle Female	skeletal muscle
13	chr21:40853800-40857200	Enhancers	Skeletal Muscle Male	skeletal muscle
14	chr21:40854400-40857600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr21:40855000-40857200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr21:40855000-40860600	Weak transcription	Psoas Muscle	Psoas
17	chr21:40855600-40856800	Enhancers	Hela-S3	cervix
18	chr21:40855600-40857600	Enhancers	Osteobl	bone
19	chr21:40855800-40857000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr21:40855800-40857000	Enhancers	Adipose Nuclei	Adipose
21	chr21:40855800-40857200	Genic enhancers	Fetal Heart	heart
22	chr21:40856200-40856800	Enhancers	Aorta	Aorta

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