Variant report

Variant	rs62219879
Chromosome Location	chr21:40278604-40278605
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:40262001..40266024-chr21:40277742..40279411,3	K562	blood:
2	chr21:40276653..40279130-chr21:40568874..40571656,2	K562	blood:
3	chr21:40271835..40274806-chr21:40278210..40280286,3	K562	blood:
4	chr21:40130024..40132037-chr21:40276501..40279158,2	K562	blood:
5	chr21:40221988..40225135-chr21:40277085..40280385,3	MCF-7	breast:
6	chr21:40276535..40278972-chr21:40279958..40281891,2	K562	blood:
7	chr21:40273169..40275089-chr21:40277742..40279439,2	MCF-7	breast:
8	chr21:40277912..40280277-chr21:40283584..40287294,3	K562	blood:
9	chr21:40204941..40207294-chr21:40276421..40279215,2	K562	blood:
10	chr21:40173449..40180758-chr21:40275825..40282486,14	MCF-7	breast:
11	chr21:40277750..40280235-chr21:40298828..40301612,2	MCF-7	breast:
12	chr21:40223431..40225086-chr21:40277290..40280274,2	MCF-7	breast:
13	chr21:40268911..40271660-chr21:40277159..40278899,2	MCF-7	breast:
14	chr21:40249695..40251882-chr21:40278200..40280440,2	MCF-7	breast:
15	chr21:40277363..40279174-chr21:40508328..40510405,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000234035	Chromatin interaction
ENSG00000157557	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs405448	0.83[EUR][1000 genomes]
rs467571	0.88[EUR][1000 genomes]
rs467967	0.88[EUR][1000 genomes]
rs468004	0.88[EUR][1000 genomes]
rs468443	0.88[EUR][1000 genomes]
rs468671	0.80[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs468959	0.88[EUR][1000 genomes]
rs468981	0.88[EUR][1000 genomes]
rs469219	0.88[EUR][1000 genomes]
rs469366	0.88[EUR][1000 genomes]
rs469554	0.88[EUR][1000 genomes]
rs469557	0.83[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs469564	0.88[EUR][1000 genomes]
rs469597	0.90[EUR][1000 genomes]
rs57966107	0.90[EUR][1000 genomes]
rs60559455	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62217833	0.80[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs62217834	0.94[EUR][1000 genomes]
rs62217840	0.92[EUR][1000 genomes]
rs62219876	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62219877	0.98[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs62219878	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[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:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40273800-40284800	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr21:40276400-40280400	Weak transcription	Gastric	stomach
3	chr21:40276600-40278800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr21:40276600-40278800	Weak transcription	Fetal Heart	heart
5	chr21:40276600-40278800	Weak transcription	Fetal Thymus	thymus
6	chr21:40276600-40279400	Weak transcription	Aorta	Aorta
7	chr21:40277000-40278800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr21:40277800-40280400	Enhancers	Fetal Stomach	stomach
9	chr21:40277800-40280400	Enhancers	Stomach Mucosa	stomach
10	chr21:40277800-40281200	Enhancers	Hela-S3	cervix
11	chr21:40277800-40287000	Enhancers	Left Ventricle	heart
12	chr21:40278000-40278800	Enhancers	Skeletal Muscle Male	skeletal muscle
13	chr21:40278000-40283400	Enhancers	Placenta	Placenta
14	chr21:40278200-40279600	Enhancers	Fetal Muscle Trunk	muscle
15	chr21:40278400-40279000	Enhancers	Esophagus	oesophagus
16	chr21:40278400-40279000	Enhancers	Sigmoid Colon	Sigmoid Colon
17	chr21:40278400-40279600	Enhancers	Fetal Muscle Leg	muscle
18	chr21:40278400-40284800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr21:40278600-40279000	Enhancers	Colonic Mucosa	Colon
20	chr21:40278600-40279000	Flanking Active TSS	Colon Smooth Muscle	Colon
21	chr21:40278600-40279000	Enhancers	Ovary	ovary
22	chr21:40278600-40279000	Enhancers	Right Atrium	heart
23	chr21:40278600-40279200	Enhancers	Small Intestine	intestine
24	chr21:40278600-40279200	Flanking Active TSS	Stomach Smooth Muscle	stomach
25	chr21:40278600-40279400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr21:40278600-40279400	Enhancers	Duodenum Mucosa	Duodenum
27	chr21:40278600-40279400	Enhancers	Lung	lung
28	chr21:40278600-40279600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr21:40278600-40279600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr21:40278600-40279600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
31	chr21:40278600-40279600	Enhancers	Pancreas	Pancrea
32	chr21:40278600-40279600	Enhancers	Psoas Muscle	Psoas
33	chr21:40278600-40279800	Enhancers	Liver	Liver
34	chr21:40278600-40279800	Enhancers	Duodenum Smooth Muscle	Duodenum
35	chr21:40278600-40280000	Enhancers	Adipose Nuclei	Adipose
36	chr21:40278600-40280000	Enhancers	Fetal Lung	lung
37	chr21:40278600-40280000	Enhancers	Rectal Mucosa Donor 29	rectum
38	chr21:40278600-40280000	Enhancers	Rectal Smooth Muscle	rectum
39	chr21:40278600-40280200	Enhancers	Fetal Intestine Large	intestine
40	chr21:40278600-40280200	Enhancers	HepG2	liver
41	chr21:40278600-40280600	Enhancers	Placenta Amnion	Placenta Amnion
42	chr21:40278600-40281200	Enhancers	HMEC	breast
43	chr21:40278600-40282600	Enhancers	Spleen	Spleen
44	chr21:40278600-40283000	Enhancers	Fetal Intestine Small	intestine
45	chr21:40278600-40283600	Enhancers	Skeletal Muscle Female	skeletal muscle
46	chr21:40278600-40284600	Enhancers	Rectal Mucosa Donor 31	rectum
47	chr21:40278600-40284800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr21:40278600-40285000	Enhancers	NHEK	skin
49	chr21:40278600-40285200	Enhancers	Right Ventricle	heart

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