Variant report

Variant	rs28653517
Chromosome Location	chr4:26910352-26910353
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10001152	1.00[AMR][1000 genomes]
rs10003072	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10004586	1.00[AMR][1000 genomes]
rs10029816	1.00[AMR][1000 genomes]
rs10031739	1.00[AMR][1000 genomes]
rs10213141	1.00[AMR][1000 genomes]
rs10213530	1.00[AMR][1000 genomes]
rs11944899	1.00[AMR][1000 genomes]
rs13434414	1.00[AMR][1000 genomes]
rs28368519	1.00[AMR][1000 genomes]
rs28371138	1.00[AMR][1000 genomes]
rs28445792	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28447383	1.00[AMR][1000 genomes]
rs28453819	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28493450	1.00[AMR][1000 genomes]
rs28626184	1.00[AMR][1000 genomes]
rs28638023	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28647178	1.00[AMR][1000 genomes]
rs28667144	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28688827	1.00[AMR][1000 genomes]
rs28690636	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28733863	1.00[AMR][1000 genomes]
rs28819422	1.00[AMR][1000 genomes]
rs28850050	1.00[AMR][1000 genomes]
rs4422408	1.00[AMR][1000 genomes]
rs56169951	1.00[AMR][1000 genomes]
rs6821940	1.00[AMR][1000 genomes]
rs6848664	1.00[AMR][1000 genomes]
rs73811393	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73811398	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73813221	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73813250	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73813253	1.00[AMR][1000 genomes]
rs9990447	1.00[AMR][1000 genomes]
rs9997247	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470021	chr4:26721578-27067027	Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv1001306	chr4:26821511-26955344	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv461312	chr4:26844674-27078376	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv593872	chr4:26844674-27078376	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv1000568	chr4:26886920-27049554	Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:26880600-26921600	Weak transcription	Fetal Muscle Trunk	muscle
2	chr4:26886600-26921600	Weak transcription	Fetal Muscle Leg	muscle
3	chr4:26898400-26914400	Weak transcription	HSMM	muscle
4	chr4:26900400-26913200	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr4:26902800-26912400	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr4:26902800-26914400	Weak transcription	Right Atrium	heart
7	chr4:26903000-26913000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr4:26904400-26913800	Weak transcription	Left Ventricle	heart
9	chr4:26905000-26910400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr4:26906000-26910600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
11	chr4:26906800-26912000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr4:26907000-26913000	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr4:26907000-26913200	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr4:26907000-26914400	Weak transcription	Psoas Muscle	Psoas
15	chr4:26907000-26917400	Weak transcription	Gastric	stomach
16	chr4:26907200-26913400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr4:26907200-26914000	Weak transcription	Duodenum Mucosa	Duodenum
18	chr4:26907200-26914400	Weak transcription	Lung	lung
19	chr4:26907200-26937800	Weak transcription	Stomach Mucosa	stomach
20	chr4:26908400-26914800	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr4:26908800-26912000	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr4:26909000-26911200	Enhancers	Brain Hippocampus Middle	brain
23	chr4:26909000-26911400	Enhancers	Primary T helper cells PMA-I stimulated	--
24	chr4:26909000-26911600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr4:26909000-26915800	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr4:26909400-26910400	Enhancers	HUES64 Cell Line	embryonic stem cell
27	chr4:26909400-26910400	Enhancers	Primary T cells fromperipheralblood	blood
28	chr4:26909400-26910600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
29	chr4:26909400-26910800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
30	chr4:26909400-26911000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr4:26909400-26912400	Enhancers	Brain Substantia Nigra	brain
32	chr4:26909600-26911600	Enhancers	Brain Angular Gyrus	brain
33	chr4:26909600-26912000	Enhancers	Brain Anterior Caudate	brain
34	chr4:26909600-26912200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr4:26909600-26913200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr4:26909600-26916600	Weak transcription	Primary hematopoietic stem cells	blood
37	chr4:26909600-26921400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr4:26909600-26923000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr4:26909800-26910800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
40	chr4:26909800-26911600	Enhancers	HMEC	breast
41	chr4:26909800-26912000	Enhancers	Ovary	ovary
42	chr4:26909800-26912200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr4:26909800-26913000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr4:26909800-26913200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr4:26909800-26921400	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr4:26910000-26910400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr4:26910000-26910400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr4:26910000-26910600	Enhancers	GM12878-XiMat	blood
49	chr4:26910000-26911000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr4:26910000-26911000	Weak transcription	Brain Inferior Temporal Lobe	brain

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