Variant report

Variant	rs58355728
Chromosome Location	chr15:40530567-40530568
allele	A/G
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	chr15:40530181-40531721	SK-N-MC	brain:	n/a	n/a

Variant related genes	Relation type
PAK6	TF binding region

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs11070254	0.87[AMR][1000 genomes]
rs12385956	0.87[AMR][1000 genomes]
rs13380113	0.87[AMR][1000 genomes]
rs28390245	0.87[AMR][1000 genomes]
rs28417868	0.87[AMR][1000 genomes]
rs28418337	1.00[AMR][1000 genomes]
rs28485685	1.00[AMR][1000 genomes]
rs28526743	0.87[AMR][1000 genomes]
rs28561898	1.00[AMR][1000 genomes]
rs28565228	1.00[AMR][1000 genomes]
rs28606396	1.00[AMR][1000 genomes]
rs28637656	1.00[AMR][1000 genomes]
rs28668026	0.87[AMR][1000 genomes]
rs28673302	1.00[AMR][1000 genomes]
rs28744626	0.87[AMR][1000 genomes]
rs28869227	0.87[AMR][1000 genomes]
rs57537959	0.83[AFR][1000 genomes]
rs60743501	1.00[AMR][1000 genomes]
rs7168394	1.00[AMR][1000 genomes]
rs73377835	0.87[AMR][1000 genomes]
rs73389489	1.00[AMR][1000 genomes]
rs73389492	1.00[AMR][1000 genomes]
rs73389507	0.87[AMR][1000 genomes]
rs73389520	0.87[AMR][1000 genomes]
rs73389531	1.00[AMR][1000 genomes]
rs73389536	0.87[AMR][1000 genomes]
rs73389540	1.00[AMR][1000 genomes]
rs73390146	1.00[AMR][1000 genomes]
rs73390155	0.87[AMR][1000 genomes]
rs73390167	1.00[AMR][1000 genomes]
rs73390168	0.87[AMR][1000 genomes]
rs73391309	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73391316	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs967945	1.00[AMR][1000 genomes]
rs9806126	0.87[AMR][1000 genomes]
rs9806144	0.87[AMR][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	nsv530816	chr15:40003136-40586792	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv904095	chr15:40525430-40591570	Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv471240	chr15:40528155-40595627	Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 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	chr15:40492800-40530800	Weak transcription	Duodenum Mucosa	Duodenum
2	chr15:40513200-40531200	Weak transcription	NHDF-Ad	bronchial
3	chr15:40513400-40530800	Weak transcription	A549	lung
4	chr15:40515400-40530600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr15:40516200-40530600	Weak transcription	Fetal Intestine Large	intestine
6	chr15:40522400-40531800	Weak transcription	Gastric	stomach
7	chr15:40524400-40530800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr15:40525200-40530800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr15:40525200-40531000	Weak transcription	Brain Anterior Caudate	brain
10	chr15:40525200-40531200	Weak transcription	Right Atrium	heart
11	chr15:40525400-40530600	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr15:40525400-40531200	Weak transcription	Adipose Nuclei	Adipose
13	chr15:40526600-40530800	Weak transcription	Thymus	Thymus
14	chr15:40527200-40530600	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr15:40527600-40530600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr15:40527600-40530600	Weak transcription	Placenta	Placenta
17	chr15:40527800-40530600	Weak transcription	Hela-S3	cervix
18	chr15:40527800-40531000	Weak transcription	K562	blood
19	chr15:40528000-40530600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr15:40528000-40530600	Weak transcription	Esophagus	oesophagus
21	chr15:40528000-40530800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr15:40528000-40530800	Weak transcription	GM12878-XiMat	blood
23	chr15:40528000-40531000	Weak transcription	Primary hematopoietic stem cells	blood
24	chr15:40528000-40531000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr15:40528200-40530600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr15:40528200-40530600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr15:40528200-40530800	Weak transcription	Primary B cells from cord blood	blood
28	chr15:40530000-40530600	Enhancers	H1 Cell Line	embryonic stem cell
29	chr15:40530200-40530600	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
30	chr15:40530200-40530600	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
31	chr15:40530400-40530600	Enhancers	Colonic Mucosa	Colon
32	chr15:40530400-40530600	Enhancers	Fetal Brain Female	brain
33	chr15:40530400-40530600	Bivalent/Poised TSS	Fetal Muscle Trunk	muscle
34	chr15:40530400-40530800	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
35	chr15:40530400-40530800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr15:40530400-40530800	Enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr15:40530400-40530800	Enhancers	Primary B cells from peripheral blood	blood
38	chr15:40530400-40530800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr15:40530400-40530800	Enhancers	Brain Germinal Matrix	brain
40	chr15:40530400-40530800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
41	chr15:40530400-40530800	Enhancers	HMEC	breast
42	chr15:40530400-40531000	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
43	chr15:40530400-40531000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr15:40530400-40531000	Bivalent Enhancer	Fetal Intestine Small	intestine
45	chr15:40530400-40531000	Enhancers	NHEK	skin
46	chr15:40530400-40531200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr15:40530400-40531200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
48	chr15:40530400-40531200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr15:40530400-40532000	Enhancers	Lung	lung

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