Variant report

Variant	rs28380652
Chromosome Location	chr4:120430952-120430953
allele	C/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	POLR2A	chr4:120430918-120431208	IMR90	lung:	n/a	n/a
2	POLR2A	chr4:120430718-120431074	HepG2	liver:	n/a	n/a
3	POLR2A	chr4:120430942-120431023	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
PDE5A	TF binding region
ENSG00000245958	TF binding region

Extended variants
information (count: 76 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10003953	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10010097	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10012406	1.00[AMR][1000 genomes]
rs10015714	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10015999	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10017842	1.00[AMR][1000 genomes]
rs10021318	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10023384	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10027735	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10028634	1.00[AMR][1000 genomes]
rs10029882	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10031328	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10032392	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10213498	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10471013	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11098519	1.00[AMR][1000 genomes]
rs11098520	1.00[AMR][1000 genomes]
rs28399227	1.00[AMR][1000 genomes]
rs28405434	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28419430	1.00[AMR][1000 genomes]
rs28436005	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28450144	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28461667	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28469881	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28470408	1.00[AMR][1000 genomes]
rs28535588	1.00[AMR][1000 genomes]
rs28576329	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28590285	1.00[AMR][1000 genomes]
rs28615474	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28622207	1.00[AMR][1000 genomes]
rs28634062	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28639494	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28639769	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28651206	1.00[AMR][1000 genomes]
rs28654414	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28665114	1.00[AMR][1000 genomes]
rs28669906	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28709577	1.00[AMR][1000 genomes]
rs28736368	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28864814	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28870820	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3872804	1.00[AMR][1000 genomes]
rs55905129	1.00[AMR][1000 genomes]
rs56191916	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57295141	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57516186	1.00[AMR][1000 genomes]
rs59116083	1.00[AMR][1000 genomes]
rs61729464	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61823285	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72918555	1.00[AMR][1000 genomes]
rs72918590	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72918597	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72920607	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72920619	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72920685	1.00[AMR][1000 genomes]
rs9307478	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9884290	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9884542	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9993996	1.00[AMR][1000 genomes]
rs9996803	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9997423	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9998244	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916641	chr4:119780023-120777320	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv1012868	chr4:120014630-120464880	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv537232	chr4:120014630-120464880	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
4	nsv427694	chr4:120250511-120501728	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv879843	chr4:120326323-120502461	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv879844	chr4:120341296-120449810	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv879846	chr4:120341296-120491714	Weak transcription Strong transcription Genic enhancers Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	nsv879845	chr4:120341296-120502461	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
9	nsv879847	chr4:120371729-120450159	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv532739	chr4:120392824-121098103	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Active TSS 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	33 gene(s)	inside rSNPs	diseases
11	esv1802153	chr4:120397829-120457682	Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv879848	chr4:120408931-120433807	Weak transcription Genic enhancers Strong transcription Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	nsv1010753	chr4:120429028-120684310	Bivalent/Poised TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
14	nsv537233	chr4:120429028-120684310	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120376400-120471600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr4:120377200-120433800	Weak transcription	Gastric	stomach
3	chr4:120377400-120439000	Weak transcription	Small Intestine	intestine
4	chr4:120377400-120439000	Weak transcription	Spleen	Spleen
5	chr4:120377600-120441000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr4:120377600-120501200	Weak transcription	Pancreas	Pancrea
7	chr4:120384400-120439200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr4:120397800-120442600	Weak transcription	Hela-S3	cervix
9	chr4:120399200-120431200	Weak transcription	Fetal Heart	heart
10	chr4:120401600-120433800	Weak transcription	Right Ventricle	heart
11	chr4:120401800-120433400	Weak transcription	Psoas Muscle	Psoas
12	chr4:120403400-120445800	Weak transcription	A549	lung
13	chr4:120408400-120433800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr4:120413800-120433800	Weak transcription	Esophagus	oesophagus
15	chr4:120414000-120438200	Strong transcription	Osteobl	bone
16	chr4:120414400-120440400	Strong transcription	Rectal Mucosa Donor 29	rectum
17	chr4:120415200-120433600	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr4:120415200-120438800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
19	chr4:120416400-120434400	Weak transcription	Brain Substantia Nigra	brain
20	chr4:120416600-120434200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr4:120416800-120436000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr4:120417200-120434400	Weak transcription	K562	blood
23	chr4:120417200-120439400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr4:120417400-120434400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr4:120417600-120445800	Weak transcription	NHEK	skin
26	chr4:120418600-120434000	Weak transcription	Colonic Mucosa	Colon
27	chr4:120419600-120439200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr4:120420200-120433000	Weak transcription	Fetal Brain Female	brain
29	chr4:120420200-120433600	Weak transcription	Primary B cells from peripheral blood	blood
30	chr4:120420200-120433600	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr4:120420200-120433600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr4:120420200-120434200	Weak transcription	Brain Cingulate Gyrus	brain
33	chr4:120420200-120434400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr4:120420200-120439000	Weak transcription	GM12878-XiMat	blood
35	chr4:120420200-120440200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr4:120420200-120440200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr4:120420200-120485400	Weak transcription	Fetal Brain Male	brain
38	chr4:120420400-120431000	Strong transcription	NHLF	lung
39	chr4:120420400-120434200	Weak transcription	HMEC	breast
40	chr4:120420400-120449600	Weak transcription	Brain Angular Gyrus	brain
41	chr4:120420600-120433600	Weak transcription	Brain Germinal Matrix	brain
42	chr4:120420800-120432600	Weak transcription	Brain Hippocampus Middle	brain
43	chr4:120420800-120434000	Weak transcription	Lung	lung
44	chr4:120420800-120434800	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr4:120421000-120434000	Weak transcription	Thymus	Thymus
46	chr4:120421000-120434200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr4:120421000-120443600	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr4:120421000-120445600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr4:120421200-120431400	Strong transcription	Fetal Lung	lung
50	chr4:120421200-120455200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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