Variant report

Variant	rs28399794
Chromosome Location	chr21:40513473-40513474
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 76 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10154057	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1041439	0.87[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs11702268	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11910971	0.82[EUR][1000 genomes]
rs13050247	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13050584	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13051430	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1541100	0.82[EUR][1000 genomes]
rs1541101	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1984748	0.80[EUR][1000 genomes]
rs2026266	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2142117	0.82[EUR][1000 genomes]
rs2150410	0.84[EUR][1000 genomes]
rs2150412	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2183574	0.87[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs2183575	0.82[EUR][1000 genomes]
rs2183576	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2225425	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2236437	0.95[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2410104	0.87[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs2410121	0.82[EUR][1000 genomes]
rs383967	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs391062	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs413078	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs425988	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs444130	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs452776	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4816619	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4818006	0.82[EUR][1000 genomes]
rs4818007	0.82[EUR][1000 genomes]
rs4818011	0.82[EUR][1000 genomes]
rs4818012	0.82[EUR][1000 genomes]
rs55885019	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56151678	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6517520	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6517524	0.87[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs6517525	0.84[EUR][1000 genomes]
rs6517529	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6517530	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6517531	0.82[EUR][1000 genomes]
rs6517532	0.82[EUR][1000 genomes]
rs6517536	0.82[EUR][1000 genomes]
rs6517539	0.82[EUR][1000 genomes]
rs6650847	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs66519408	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs66746936	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67212994	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67382266	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67649754	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs68069991	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs68086041	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs68114370	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs718225	0.82[EUR][1000 genomes]
rs7275773	0.82[EUR][1000 genomes]
rs7276559	0.82[EUR][1000 genomes]
rs7276698	0.82[EUR][1000 genomes]
rs7282029	0.84[EUR][1000 genomes]
rs7282724	0.82[EUR][1000 genomes]
rs7282947	0.82[EUR][1000 genomes]
rs7283439	0.80[EUR][1000 genomes]
rs7283652	0.82[EUR][1000 genomes]
rs8127391	0.82[EUR][1000 genomes]
rs8127537	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8130774	0.82[EUR][1000 genomes]
rs8131091	0.82[EUR][1000 genomes]
rs8131263	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8132230	0.82[EUR][1000 genomes]
rs914157	0.82[EUR][1000 genomes]
rs971229	0.82[EUR][1000 genomes]
rs973521	0.82[EUR][1000 genomes]
rs9975410	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9978591	0.82[EUR][1000 genomes]
rs9982122	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[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	nsv1061831	chr21:40376316-40583555	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv544443	chr21:40376316-40583555	Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	esv3395554	chr21:40512728-40517052	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40509400-40513600	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr21:40509800-40513600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr21:40509800-40513800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr21:40509800-40515800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr21:40510600-40515000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr21:40512000-40514200	Enhancers	Fetal Thymus	thymus
7	chr21:40512800-40514200	Enhancers	Sigmoid Colon	Sigmoid Colon
8	chr21:40513000-40514000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr21:40513000-40514000	Enhancers	Thymus	Thymus
10	chr21:40513200-40513800	Enhancers	Fetal Muscle Leg	muscle
11	chr21:40513200-40513800	Enhancers	Stomach Mucosa	stomach
12	chr21:40513200-40514000	Enhancers	HSMMtube	muscle
13	chr21:40513200-40514200	Enhancers	Placenta	Placenta
14	chr21:40513400-40514000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr21:40513400-40514000	Enhancers	Fetal Lung	lung
16	chr21:40513400-40514000	Flanking Active TSS	NHDF-Ad	bronchial
17	chr21:40513400-40514400	Enhancers	Rectal Mucosa Donor 31	rectum

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