Variant report

Variant	rs9976408
Chromosome Location	chr21:40356624-40356625
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:40338908..40342135-chr21:40355414..40359541,3	K562	blood:
2	chr21:40347269..40350554-chr21:40353946..40356975,3	K562	blood:
3	chr21:40177341..40179310-chr21:40356507..40359292,3	K562	blood:
4	21:40348344-40365490..21:40748850-40752541	Hela-S3	cervix:
5	chr21:40356286..40358382-chr21:40363129..40364853,2	K562	blood:

Variant related genes	Relation type
ENSG00000182093	Chromatin interaction
ENSG00000227406	Chromatin interaction
ENSG00000232837	Chromatin interaction
ENSG00000157557	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs2836806	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836807	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836808	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28673525	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4817978	0.94[ASN][1000 genomes]
rs4817979	0.80[ASN][1000 genomes]
rs58301407	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60329156	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60789326	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73364803	0.98[EUR][1000 genomes]
rs9976856	0.92[EUR][1000 genomes]
rs9976927	0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9978603	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9985005	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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	nsv1062425	chr21:40172471-40380976	Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv544442	chr21:40172471-40380976	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv587477	chr21:40228920-40512004	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40332000-40356800	Weak transcription	Right Atrium	heart
2	chr21:40351000-40359600	Enhancers	Primary hematopoietic stem cells	blood
3	chr21:40351600-40357200	Weak transcription	Lung	lung
4	chr21:40352400-40370000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr21:40353200-40356800	Enhancers	Primary hematopoietic stem cells short term culture	blood
6	chr21:40353600-40359600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr21:40353800-40358400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr21:40354000-40359400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr21:40354400-40358600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr21:40354600-40356800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr21:40354600-40357400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr21:40354600-40359000	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr21:40354600-40359200	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr21:40354600-40359400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr21:40354600-40359400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr21:40354600-40364600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr21:40354800-40356800	Weak transcription	Placenta	Placenta
18	chr21:40354800-40359200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr21:40354800-40359400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr21:40355000-40359000	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr21:40355200-40359600	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr21:40355600-40356800	Enhancers	Skeletal Muscle Female	skeletal muscle
23	chr21:40355800-40358400	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr21:40355800-40358800	Enhancers	Fetal Heart	heart
25	chr21:40355800-40359200	Enhancers	HSMM	muscle
26	chr21:40355800-40360000	Enhancers	HSMMtube	muscle
27	chr21:40355800-40360400	Enhancers	Fetal Muscle Leg	muscle
28	chr21:40356000-40356800	Enhancers	Muscle Satellite Cultured Cells	--
29	chr21:40356000-40356800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr21:40356000-40356800	Enhancers	Thymus	Thymus
31	chr21:40356000-40356800	Enhancers	NHDF-Ad	bronchial
32	chr21:40356000-40357600	Enhancers	NHLF	lung
33	chr21:40356000-40357800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr21:40356000-40358000	Enhancers	Fetal Muscle Trunk	muscle
35	chr21:40356000-40358000	Enhancers	Fetal Thymus	thymus
36	chr21:40356000-40358200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr21:40356000-40358200	Enhancers	Primary monocytes fromperipheralblood	blood
38	chr21:40356000-40358200	Enhancers	Esophagus	oesophagus
39	chr21:40356000-40358600	Enhancers	Spleen	Spleen
40	chr21:40356000-40358600	Flanking Active TSS	Dnd41	blood
41	chr21:40356000-40358600	Enhancers	HMEC	breast
42	chr21:40356000-40358800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr21:40356000-40369400	Enhancers	Left Ventricle	heart
44	chr21:40356200-40356800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr21:40356200-40356800	Enhancers	Monocytes-CD14+_RO01746	blood
46	chr21:40356200-40357200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr21:40356200-40357600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr21:40356200-40357600	Enhancers	Skeletal Muscle Male	skeletal muscle
49	chr21:40356200-40357800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr21:40356200-40358000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland

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