Variant report

Variant	rs62219887
Chromosome Location	chr21:40288055-40288056
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA2	chr21:40287989-40289464	HepG2	liver:	n/a	chr21:40288529-40288541 chr21:40288533-40288545
2	FOXA1	chr21:40288055-40288499	HepG2	liver:	n/a	n/a
3	POLR2A	chr21:40288045-40288519	HepG2	liver:	n/a	n/a
4	HEY1	chr21:40287974-40288508	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:40287929..40293314-chr21:40293735..40297286,6	MCF-7	breast:
2	chr21:40284319..40286994-chr21:40287410..40290076,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000234035	TF binding region

Extended variants
information (count: 6 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs62219886	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9979503	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	nsv587479	chr21:40282556-40297536	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40284800-40289200	Weak transcription	Small Intestine	intestine
2	chr21:40285600-40288200	Enhancers	Fetal Intestine Large	intestine
3	chr21:40285600-40288600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr21:40285800-40290600	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr21:40285800-40292000	Enhancers	Fetal Intestine Small	intestine
6	chr21:40285800-40292400	Weak transcription	Aorta	Aorta
7	chr21:40286000-40289600	Enhancers	Stomach Mucosa	stomach
8	chr21:40286000-40292600	Enhancers	Hela-S3	cervix
9	chr21:40286400-40288400	Enhancers	Rectal Mucosa Donor 31	rectum
10	chr21:40286400-40288800	Enhancers	Fetal Lung	lung
11	chr21:40286400-40290600	Weak transcription	Fetal Kidney	kidney
12	chr21:40286600-40290400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr21:40286800-40292600	Weak transcription	Colonic Mucosa	Colon
14	chr21:40287000-40288200	Weak transcription	HMEC	breast
15	chr21:40287000-40289200	Weak transcription	Liver	Liver
16	chr21:40287000-40290600	Weak transcription	Ovary	ovary
17	chr21:40287000-40292400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr21:40287000-40292600	Weak transcription	Left Ventricle	heart
19	chr21:40287000-40295800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr21:40287000-40297000	Weak transcription	Lung	lung
21	chr21:40287000-40297400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr21:40287000-40297400	Weak transcription	Right Atrium	heart
23	chr21:40287000-40305400	Weak transcription	Gastric	stomach
24	chr21:40287200-40288200	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr21:40287200-40288600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr21:40287200-40289000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr21:40287200-40289000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr21:40287200-40290400	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr21:40287200-40290400	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr21:40287200-40291200	Weak transcription	Psoas Muscle	Psoas
31	chr21:40287200-40292400	Weak transcription	Rectal Smooth Muscle	rectum
32	chr21:40287200-40292600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr21:40287200-40292600	Weak transcription	Fetal Muscle Leg	muscle
34	chr21:40287200-40292600	Weak transcription	Stomach Smooth Muscle	stomach
35	chr21:40287200-40292600	Weak transcription	HSMMtube	muscle
36	chr21:40287200-40292800	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr21:40287200-40297000	Weak transcription	Esophagus	oesophagus
38	chr21:40287800-40288200	Enhancers	HUES6 Cell Line	embryonic stem cell
39	chr21:40287800-40291200	Weak transcription	Thymus	Thymus
40	chr21:40288000-40288200	Enhancers	Brain Substantia Nigra	brain
41	chr21:40288000-40288400	Flanking Active TSS	HepG2	liver
42	chr21:40288000-40289000	Weak transcription	Fetal Thymus	thymus
43	chr21:40288000-40289400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr21:40288000-40290800	Weak transcription	Duodenum Mucosa	Duodenum
45	chr21:40288000-40292600	Weak transcription	Skeletal Muscle Male	skeletal muscle

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