Variant report

Variant	rs58403754
Chromosome Location	chr15:75290822-75290823
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:75289096..75291038-chr15:75311135..75313518,2	K562	blood:
2	chr15:75286777..75288532-chr15:75290175..75292211,2	K562	blood:
3	chr15:75286200..75292858-chr15:75303462..75309796,11	MCF-7	breast:
4	chr15:75289676..75292332-chr15:75492915..75494669,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198794	Chromatin interaction
ENSG00000167173	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs11072519	0.82[AMR][1000 genomes]
rs12591994	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12592477	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12593476	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12593542	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12594117	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2289582	0.90[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2304904	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28394281	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3812943	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3812946	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3816261	0.82[EUR][1000 genomes]
rs3910748	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55877218	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56828495	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56970592	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58068887	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58294763	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58645417	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59094290	0.90[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs61166993	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6495135	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6495136	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6495137	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6495138	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6495140	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6495142	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7163390	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7166105	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7167415	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7168638	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7172065	0.92[EUR][1000 genomes]
rs7172715	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7172989	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7173218	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7174129	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7177109	0.81[EUR][1000 genomes]
rs7179097	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7181942	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7182286	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7342591	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7342601	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73436579	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73436586	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73438537	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73438554	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs74023908	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs74025863	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8031545	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8034149	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8036573	0.90[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs8040961	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9672926	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9672995	0.87[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs9672996	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9673012	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9788648	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv569993	chr15:75242155-75483752	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
2	nsv542435	chr15:75271788-75321117	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs58403754	PPCDC	cis	Adipose Subcutaneous	GTEx
rs58403754	SCAMP5	cis	Thyroid	GTEx
rs58403754	SCAMP5	cis	Esophagus Mucosa	GTEx
rs58403754	SCAMP5	cis	Artery Tibial	GTEx

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75289000-75291000	Weak transcription	Fetal Intestine Large	intestine
2	chr15:75289000-75315800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr15:75289400-75291000	Weak transcription	Fetal Intestine Small	intestine
4	chr15:75289400-75291400	Enhancers	Fetal Brain Male	brain
5	chr15:75289400-75299600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr15:75289400-75305000	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr15:75289400-75305000	Weak transcription	Brain Substantia Nigra	brain
8	chr15:75289400-75305600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr15:75289400-75315400	Weak transcription	Fetal Kidney	kidney
10	chr15:75289600-75292200	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr15:75289600-75304000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr15:75289600-75305400	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr15:75289800-75293800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr15:75289800-75296600	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr15:75289800-75298800	Weak transcription	Right Atrium	heart
16	chr15:75289800-75299200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr15:75289800-75299600	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr15:75289800-75304000	Weak transcription	Brain Hippocampus Middle	brain
19	chr15:75290000-75303600	Weak transcription	Brain Angular Gyrus	brain
20	chr15:75290000-75303800	Weak transcription	Brain Cingulate Gyrus	brain
21	chr15:75290000-75304400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr15:75290000-75304400	Weak transcription	HepG2	liver
23	chr15:75290000-75309400	Weak transcription	Gastric	stomach
24	chr15:75290000-75316000	Weak transcription	Small Intestine	intestine
25	chr15:75290200-75291800	Genic enhancers	Fetal Brain Female	brain
26	chr15:75290200-75299200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr15:75290200-75302400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr15:75290400-75291000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr15:75290400-75292600	Weak transcription	Duodenum Mucosa	Duodenum
30	chr15:75290400-75296000	Weak transcription	Brain Germinal Matrix	brain
31	chr15:75290400-75304800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr15:75290400-75304800	Weak transcription	Brain Anterior Caudate	brain
33	chr15:75290600-75291000	Weak transcription	Pancreas	Pancrea
34	chr15:75290600-75304400	Weak transcription	Fetal Stomach	stomach
35	chr15:75290800-75291200	Weak transcription	Brain Inferior Temporal Lobe	brain

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