Variant report

Variant	rs2223028
Chromosome Location	chr21:40810373-40810374
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:40796099..40798923-chr21:40809291..40810849,2	MCF-7	breast:
2	chr21:40808402..40815127-chr21:40815513..40821149,12	K562	blood:
3	chr21:40806088..40810379-chr21:40811300..40813801,4	MCF-7	breast:
4	chr21:40554325..40556073-chr21:40808791..40811765,2	K562	blood:
5	chr21:40808687..40811589-chr21:40816980..40819320,3	K562	blood:

Variant related genes	Relation type
ENSG00000182093	Chromatin interaction
ENSG00000183527	Chromatin interaction
ENSG00000185437	Chromatin interaction
ENSG00000157578	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs11575939	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16997618	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2065313	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2205200	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2205201	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2246078	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2410128	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837009	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2837015	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2837017	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2837018	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2837019	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837020	0.95[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2837021	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837022	1.00[ASN][1000 genomes]
rs2837023	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837024	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837025	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837026	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837029	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837030	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837031	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837032	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837034	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837036	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837037	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837039	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2837040	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2840267	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4281987	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56812456	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56866897	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58900137	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs596289	0.80[ASN][1000 genomes]
rs61342945	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7275686	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7276575	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7276981	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7277627	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7279753	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73365952	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73367928	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73367958	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73367962	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73367974	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73367976	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73906032	0.81[ASN][1000 genomes]
rs73906033	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73906034	0.81[ASN][1000 genomes]
rs940625	0.80[ASN][1000 genomes]
rs9680443	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs2223028	SH3BGR	cis	Artery Tibial	GTEx
rs2223028	LCA5L	cis	Thyroid	GTEx
rs2223028	LCA5L	cis	Skin Sun Exposed Lower leg	GTEx
rs2223028	WRB	cis	lung	GTEx
rs2223028	WRB	cis	Adipose Subcutaneous	GTEx
rs2223028	SH3BGR	cis	Skin Sun Exposed Lower leg	GTEx
rs2223028	LCA5L	cis	Esophagus Muscularis	GTEx
rs2223028	LCA5L	cis	Artery Aorta	GTEx
rs2223028	LCA5L	cis	lung	GTEx
rs2223028	LCA5L	cis	Nerve Tibial	GTEx
rs2223028	WRB	cis	Artery Tibial	GTEx
rs2223028	WRB	cis	Nerve Tibial	GTEx
rs2223028	WRB	cis	Skin Sun Exposed Lower leg	GTEx
rs2223028	LCA5L	cis	Artery Tibial	GTEx

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40778200-40816600	Weak transcription	Pancreas	Pancrea
2	chr21:40778400-40816600	Weak transcription	Left Ventricle	heart
3	chr21:40781200-40811000	Weak transcription	Aorta	Aorta
4	chr21:40781200-40813000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr21:40781200-40813200	Weak transcription	HSMMtube	muscle
6	chr21:40802000-40813800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr21:40802600-40816200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr21:40802600-40816600	Weak transcription	Right Atrium	heart
9	chr21:40802800-40814000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr21:40809200-40813800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr21:40809400-40816400	Weak transcription	Stomach Smooth Muscle	stomach
12	chr21:40809800-40816600	Weak transcription	Skeletal Muscle Female	skeletal muscle

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