Variant report

Variant	rs9672996
Chromosome Location	chr15:75297671-75297672
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs11072519	0.82[AMR][1000 genomes]
rs12591175	0.84[EUR][1000 genomes]
rs12591994	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12592477	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12593476	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12593542	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12594117	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2289582	0.90[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2304904	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28394281	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3812943	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3812946	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3816261	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3910748	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55877218	0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56828495	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56970592	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58068887	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58294763	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58403754	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58645417	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59094290	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs59303424	0.80[ASN][1000 genomes]
rs61166993	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6495135	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6495136	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6495137	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6495138	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6495140	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6495142	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6495146	0.80[ASN][1000 genomes]
rs7163390	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7166105	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7167415	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7168638	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7172065	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7172715	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7172989	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7173218	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7174129	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7177109	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7179097	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7181942	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7182286	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72475969	0.80[ASN][1000 genomes]
rs7342591	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7342601	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73436579	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73436586	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73438537	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73438554	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73438569	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs74023908	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs74023935	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs74025863	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8031545	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8034149	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8036573	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs8039433	0.80[ASN][1000 genomes]
rs8040961	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9672926	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9672995	0.87[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs9673012	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9788648	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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
rs9672996	SCAMP5	cis	Esophagus Mucosa	GTEx
rs9672996	PPCDC	cis	Adipose Subcutaneous	GTEx
rs9672996	SCAMP5	cis	Thyroid	GTEx
rs9672996	SCAMP5	cis	Artery Tibial	GTEx

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75289000-75315800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:75289400-75299600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr15:75289400-75305000	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr15:75289400-75305000	Weak transcription	Brain Substantia Nigra	brain
5	chr15:75289400-75305600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr15:75289400-75315400	Weak transcription	Fetal Kidney	kidney
7	chr15:75289600-75304000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr15:75289600-75305400	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr15:75289800-75298800	Weak transcription	Right Atrium	heart
10	chr15:75289800-75299200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr15:75289800-75299600	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr15:75289800-75304000	Weak transcription	Brain Hippocampus Middle	brain
13	chr15:75290000-75303600	Weak transcription	Brain Angular Gyrus	brain
14	chr15:75290000-75303800	Weak transcription	Brain Cingulate Gyrus	brain
15	chr15:75290000-75304400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr15:75290000-75304400	Weak transcription	HepG2	liver
17	chr15:75290000-75309400	Weak transcription	Gastric	stomach
18	chr15:75290000-75316000	Weak transcription	Small Intestine	intestine
19	chr15:75290200-75299200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr15:75290200-75302400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr15:75290400-75304800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr15:75290400-75304800	Weak transcription	Brain Anterior Caudate	brain
23	chr15:75290600-75304400	Weak transcription	Fetal Stomach	stomach
24	chr15:75291200-75297800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr15:75291400-75299600	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr15:75291400-75305400	Weak transcription	Fetal Brain Male	brain
27	chr15:75291800-75299000	Weak transcription	GM12878-XiMat	blood
28	chr15:75292000-75305000	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr15:75292600-75305400	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr15:75293000-75304000	Weak transcription	Fetal Intestine Large	intestine
31	chr15:75293200-75315800	Weak transcription	Duodenum Mucosa	Duodenum
32	chr15:75294600-75312200	Weak transcription	Adipose Nuclei	Adipose
33	chr15:75294600-75315600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr15:75296000-75297800	Strong transcription	Brain Germinal Matrix	brain
35	chr15:75296400-75297800	Strong transcription	Fetal Intestine Small	intestine
36	chr15:75296800-75302000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr15:75296800-75303600	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr15:75297200-75304600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr15:75297400-75305000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr15:75297600-75298200	Enhancers	Pancreas	Pancrea
41	chr15:75297600-75303800	Weak transcription	Fetal Brain Female	brain

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