Variant report

Variant	rs28690432
Chromosome Location	chr21:17846681-17846682
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:17840645..17843394-chr21:17845243..17848250,3	MCF-7	breast:

Extended variants
information (count: 105 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs10470096	1.00[ASN][1000 genomes]
rs10470198	1.00[ASN][1000 genomes]
rs10470199	1.00[ASN][1000 genomes]
rs10470200	0.88[ASN][1000 genomes]
rs13433398	1.00[ASN][1000 genomes]
rs13433444	1.00[ASN][1000 genomes]
rs2039242	1.00[ASN][1000 genomes]
rs2039243	1.00[ASN][1000 genomes]
rs2039244	1.00[ASN][1000 genomes]
rs2823827	0.81[AMR][1000 genomes]
rs2823828	0.81[AMR][1000 genomes]
rs2823830	0.81[AMR][1000 genomes]
rs2823832	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2823833	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2823834	1.00[AMR][1000 genomes]
rs2823835	1.00[AMR][1000 genomes]
rs2823836	1.00[ASN][1000 genomes]
rs2823837	1.00[ASN][1000 genomes]
rs28407677	0.82[ASN][1000 genomes]
rs28415058	1.00[ASN][1000 genomes]
rs28433186	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28526796	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28608983	1.00[ASN][1000 genomes]
rs28643005	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28648637	1.00[ASN][1000 genomes]
rs28840743	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28844023	0.82[ASN][1000 genomes]
rs28858813	0.88[ASN][1000 genomes]
rs28875621	1.00[AMR][1000 genomes]
rs28896613	0.82[ASN][1000 genomes]
rs2896759	0.81[AMR][1000 genomes]
rs2896760	1.00[ASN][1000 genomes]
rs57055406	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57523013	1.00[AMR][1000 genomes]
rs57659737	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58072187	1.00[AMR][1000 genomes]
rs58225448	1.00[ASN][1000 genomes]
rs58236716	1.00[ASN][1000 genomes]
rs58304651	1.00[AMR][1000 genomes]
rs58640456	1.00[AMR][1000 genomes]
rs59959567	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60754236	1.00[AMR][1000 genomes]
rs60925168	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61549904	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73363411	1.00[AMR][1000 genomes]
rs73363422	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73363426	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73368523	1.00[AMR][1000 genomes]
rs73380342	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73380344	1.00[AMR][1000 genomes]
rs73891591	1.00[ASN][1000 genomes]
rs73891592	1.00[ASN][1000 genomes]
rs73893713	1.00[ASN][1000 genomes]
rs8132964	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9305766	0.88[ASN][1000 genomes]
rs9305767	1.00[ASN][1000 genomes]
rs9305768	1.00[ASN][1000 genomes]
rs9305769	1.00[ASN][1000 genomes]
rs9974386	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9974447	0.82[ASN][1000 genomes]
rs9974519	1.00[ASN][1000 genomes]
rs9975047	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9975202	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9975284	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9975582	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9975640	1.00[ASN][1000 genomes]
rs9976077	1.00[ASN][1000 genomes]
rs9976648	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9976729	0.82[ASN][1000 genomes]
rs9976887	1.00[ASN][1000 genomes]
rs9977372	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9977640	0.82[ASN][1000 genomes]
rs9977666	0.82[ASN][1000 genomes]
rs9978828	1.00[ASN][1000 genomes]
rs9979222	1.00[ASN][1000 genomes]
rs9979766	0.88[ASN][1000 genomes]
rs9979904	0.88[ASN][1000 genomes]
rs9980133	1.00[ASN][1000 genomes]
rs9980149	0.94[ASN][1000 genomes]
rs9980549	0.82[ASN][1000 genomes]
rs9980810	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9980959	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9981432	0.82[ASN][1000 genomes]
rs9981465	0.94[ASN][1000 genomes]
rs9981657	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9981699	1.00[ASN][1000 genomes]
rs9982188	0.82[ASN][1000 genomes]
rs9982511	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9982641	1.00[ASN][1000 genomes]
rs9982850	1.00[ASN][1000 genomes]
rs9983223	1.00[ASN][1000 genomes]
rs9983295	1.00[ASN][1000 genomes]
rs9983298	1.00[ASN][1000 genomes]
rs9983466	1.00[ASN][1000 genomes]
rs9984183	1.00[ASN][1000 genomes]
rs9984263	1.00[ASN][1000 genomes]
rs9984639	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9984788	1.00[ASN][1000 genomes]
rs9984970	1.00[EUR][1000 genomes]
rs9985004	1.00[ASN][1000 genomes]
rs9985090	0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9985151	1.00[EUR][1000 genomes];0.88[ASN][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	nsv1064857	chr21:17628760-18533131	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	345 gene(s)	inside rSNPs	diseases
2	nsv544382	chr21:17628760-18533131	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	345 gene(s)	inside rSNPs	diseases
3	nsv913416	chr21:17728224-17863882	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:17836800-17848400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr21:17836800-17848600	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr21:17837400-17848800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr21:17838000-17850200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr21:17840400-17848200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr21:17840400-17860800	Weak transcription	HUVEC	blood vessel
7	chr21:17841000-17881800	Weak transcription	Hela-S3	cervix
8	chr21:17841400-17848200	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr21:17845600-17847600	Enhancers	Adipose Nuclei	Adipose
10	chr21:17845800-17846800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr21:17845800-17846800	Enhancers	Fetal Heart	heart
12	chr21:17845800-17846800	Enhancers	Skeletal Muscle Male	skeletal muscle
13	chr21:17845800-17847000	Enhancers	Brain Anterior Caudate	brain
14	chr21:17846000-17849400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr21:17846200-17846800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr21:17846200-17846800	Enhancers	Brain Hippocampus Middle	brain
17	chr21:17846200-17846800	Enhancers	Fetal Lung	lung
18	chr21:17846200-17846800	Enhancers	Skeletal Muscle Female	skeletal muscle
19	chr21:17846200-17847000	Enhancers	Osteobl	bone
20	chr21:17846200-17847600	Enhancers	Brain Cingulate Gyrus	brain
21	chr21:17846200-17847600	Enhancers	Brain Substantia Nigra	brain
22	chr21:17846400-17846800	Enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr21:17846400-17846800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr21:17846400-17846800	Enhancers	Rectal Smooth Muscle	rectum
25	chr21:17846400-17847000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr21:17846400-17847000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr21:17846400-17847000	Enhancers	NH-A	brain
28	chr21:17846400-17847600	Enhancers	Brain Angular Gyrus	brain
29	chr21:17846600-17848600	Weak transcription	Colon Smooth Muscle	Colon
30	chr21:17846600-17848800	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr21:17846600-17848800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr21:17846600-17859400	Weak transcription	Ovary	ovary

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