Variant report

Variant	rs28688005
Chromosome Location	chr5:142484225-142484226
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	chr5:142480535..142484269-chr5:142501795..142505704,3	K562	blood:

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10044668	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10045128	1.00[EUR][1000 genomes]
rs10051655	1.00[EUR][1000 genomes]
rs10056044	1.00[EUR][1000 genomes]
rs10065814	1.00[AFR][1000 genomes]
rs10074187	1.00[EUR][1000 genomes]
rs10076583	1.00[EUR][1000 genomes]
rs10080138	1.00[EUR][1000 genomes]
rs10155562	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10214217	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10477199	1.00[EUR][1000 genomes]
rs10477201	1.00[AFR][1000 genomes]
rs10477202	1.00[EUR][1000 genomes]
rs11167803	0.88[AFR][1000 genomes]
rs11951777	1.00[EUR][1000 genomes]
rs12332305	1.00[EUR][1000 genomes]
rs13356063	0.98[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2108645	1.00[EUR][1000 genomes]
rs2963146	1.00[EUR][1000 genomes]
rs58817012	1.00[EUR][1000 genomes]
rs60473595	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs60477396	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61287676	1.00[AFR][1000 genomes]
rs7702357	1.00[EUR][1000 genomes]
rs9324901	0.89[AMR][1000 genomes]
rs9324902	1.00[EUR][1000 genomes]
rs9324906	1.00[AFR][1000 genomes];1.00[EUR][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	nsv830511	chr5:142335447-142496694	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1025662	chr5:142345454-142498236	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv522807	chr5:142417658-142529960	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:142449400-142487600	Weak transcription	Liver	Liver
2	chr5:142450000-142497000	Weak transcription	Primary B cells from cord blood	blood
3	chr5:142458000-142488400	Weak transcription	Gastric	stomach
4	chr5:142463200-142513600	Weak transcription	Thymus	Thymus
5	chr5:142467200-142485400	Weak transcription	HepG2	liver
6	chr5:142467800-142485000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr5:142474000-142488000	Weak transcription	Fetal Intestine Large	intestine
8	chr5:142474000-142489400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr5:142474000-142489800	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr5:142474000-142490400	Weak transcription	Fetal Intestine Small	intestine
11	chr5:142474200-142490000	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr5:142474400-142488000	Weak transcription	Stomach Mucosa	stomach
13	chr5:142474400-142489600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr5:142474400-142527200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr5:142476200-142491400	Weak transcription	Esophagus	oesophagus
16	chr5:142479200-142503600	Weak transcription	Fetal Thymus	thymus
17	chr5:142480400-142487400	Weak transcription	Duodenum Mucosa	Duodenum
18	chr5:142480400-142498600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr5:142480600-142486400	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr5:142480600-142500600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr5:142481000-142491800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr5:142481000-142500600	Weak transcription	Dnd41	blood
23	chr5:142481200-142485200	Weak transcription	Pancreas	Pancrea
24	chr5:142481600-142488000	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr5:142481800-142489400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr5:142482000-142491400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr5:142482000-142504200	Weak transcription	Aorta	Aorta
28	chr5:142482200-142485200	Weak transcription	Lung	lung
29	chr5:142482200-142486400	Weak transcription	Psoas Muscle	Psoas
30	chr5:142482200-142487800	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr5:142482200-142488400	Weak transcription	Brain Anterior Caudate	brain
32	chr5:142482200-142491400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr5:142482200-142491400	Weak transcription	Placenta	Placenta
34	chr5:142482200-142499000	Weak transcription	Fetal Stomach	stomach
35	chr5:142482400-142485200	Weak transcription	HSMM	muscle
36	chr5:142482400-142486400	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr5:142482400-142486600	Weak transcription	Right Ventricle	heart
38	chr5:142482400-142488200	Weak transcription	Brain Cingulate Gyrus	brain
39	chr5:142482400-142489800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr5:142482400-142489800	Weak transcription	Primary neutrophils fromperipheralblood	blood
41	chr5:142482400-142496600	Weak transcription	Brain Substantia Nigra	brain
42	chr5:142482600-142485600	Weak transcription	Fetal Muscle Leg	muscle
43	chr5:142482600-142485600	Weak transcription	Left Ventricle	heart
44	chr5:142482600-142485600	Weak transcription	NHDF-Ad	bronchial
45	chr5:142482600-142486000	Weak transcription	Fetal Heart	heart
46	chr5:142482600-142489800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr5:142482600-142489800	Weak transcription	Brain Angular Gyrus	brain
48	chr5:142482600-142489800	Weak transcription	Osteobl	bone
49	chr5:142482600-142490200	Weak transcription	Brain Hippocampus Middle	brain
50	chr5:142482600-142490400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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