Variant report

Variant	rs4525456
Chromosome Location	chr15:76920316-76920317
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 118 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10444858	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1116535	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1125932	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12148452	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12148877	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12437627	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12438077	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12438186	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12438540	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12440151	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12441247	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs12441550	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12594577	0.86[EUR][1000 genomes]
rs12595313	0.83[AFR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12900494	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12902174	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12902452	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12903553	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12908421	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12911987	0.83[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs1471780	0.83[AFR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1838048	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1838050	0.90[ASN][1000 genomes]
rs1867197	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1874944	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1946650	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2083762	0.91[ASN][1000 genomes]
rs2120108	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2304920	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2404733	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2404736	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2404737	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34060246	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34272342	0.80[AFR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34287706	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34478400	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34639578	0.90[ASN][1000 genomes]
rs34707035	0.86[ASN][1000 genomes]
rs34924128	0.83[AFR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35077207	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35138393	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35195096	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35395069	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35498563	0.83[AFR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35566346	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs36070630	0.85[AFR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3816266	0.88[AFR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4886496	0.82[ASN][1000 genomes]
rs4886813	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4886817	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4886822	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4886824	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4886825	0.86[ASN][1000 genomes]
rs55676827	0.83[AFR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56193230	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56351018	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs57178708	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58361452	0.83[AFR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58511211	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs58973160	0.88[AFR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59088060	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs60912217	0.83[ASN][1000 genomes]
rs66754747	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs66986092	0.81[AFR][1000 genomes]
rs67010831	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs67204011	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs67570291	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs67920045	0.85[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs71405216	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs71405222	0.85[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs71405223	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7163397	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7164813	0.81[AFR][1000 genomes]
rs7169394	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7174953	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72738889	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7342603	0.83[AFR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7350777	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7495566	0.80[EUR][1000 genomes]
rs8024476	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8036703	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8037005	0.85[AFR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8043474	0.81[AFR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9646213	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:34 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv542439	chr15:76762161-77196336	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
2	esv3440794	chr15:76764595-77571114	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv904400	chr15:76772062-77085283	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1053924	chr15:76803849-77089079	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
5	nsv471254	chr15:76811390-76978139	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
6	nsv570021	chr15:76813920-76978139	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
7	nsv570022	chr15:76816015-76978139	ZNF genes & repeats Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
8	nsv904401	chr15:76816015-77085283	Strong transcription Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
9	nsv1042089	chr15:76855098-77016127	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
10	nsv904402	chr15:76863023-76930805	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
11	esv2830013	chr15:76863023-77176158	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
12	nsv1042623	chr15:76863437-76999030	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
13	nsv1039269	chr15:76863437-77057021	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
14	nsv904403	chr15:76869929-76951040	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
15	nsv904404	chr15:76869929-77033934	Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
16	nsv904405	chr15:76869929-77047915	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
17	nsv904406	chr15:76869929-77085283	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
18	nsv904407	chr15:76869929-77121196	Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
19	nsv1052133	chr15:76878362-76962756	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
20	esv1815271	chr15:76883346-76930805	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
21	nsv570023	chr15:76884127-76978139	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
22	nsv904408	chr15:76884127-77085283	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
23	esv1824106	chr15:76891342-76930805	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
24	nsv1046858	chr15:76892097-77020971	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
25	nsv542440	chr15:76892097-77020971	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
26	nsv1043066	chr15:76892097-77057021	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
27	nsv542441	chr15:76892097-77057021	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
28	nsv1046137	chr15:76892097-77196336	ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
29	nsv542442	chr15:76892097-77196336	ZNF genes & repeats Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
30	nsv904409	chr15:76893186-77033934	Strong transcription ZNF genes & repeats Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
31	nsv904410	chr15:76893186-77047915	ZNF genes & repeats Enhancers Strong transcription Active TSS Genic enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
32	nsv904411	chr15:76893186-77085283	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
33	nsv570109	chr15:76907376-76978139	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
34	nsv904412	chr15:76910031-77085283	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4525456	SCAPER	cis	Thyroid	GTEx
rs4525456	SCAPER	cis	Artery Tibial	GTEx
rs4525456	SCAPER	Cis_1M	lymphoblastoid	RTeQTL
rs4525456	SCAPER	cis	Nerve Tibial	GTEx
rs4525456	SCAPER	cis	lung	GTEx

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:76882200-76991400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr15:76898400-76981000	Weak transcription	Pancreas	Pancrea
3	chr15:76902600-76992000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr15:76902800-76926400	Weak transcription	Dnd41	blood
5	chr15:76903400-76940400	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr15:76904000-76927800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr15:76904400-76923600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr15:76904800-76939800	Weak transcription	Aorta	Aorta
9	chr15:76905000-76941000	Weak transcription	Ovary	ovary
10	chr15:76906000-76946800	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr15:76908600-76928200	Weak transcription	Duodenum Mucosa	Duodenum
12	chr15:76908800-76928400	Weak transcription	Psoas Muscle	Psoas
13	chr15:76910000-76964200	Weak transcription	Brain Hippocampus Middle	brain
14	chr15:76910200-76926000	Weak transcription	Esophagus	oesophagus
15	chr15:76910200-76941000	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr15:76910200-76959400	Weak transcription	Brain Substantia Nigra	brain
17	chr15:76911400-76990800	Weak transcription	Placenta	Placenta
18	chr15:76911600-76928600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr15:76914000-76928200	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr15:76914000-76928600	Weak transcription	Liver	Liver
21	chr15:76914000-76939800	Weak transcription	Left Ventricle	heart
22	chr15:76914000-76952600	Weak transcription	Brain Angular Gyrus	brain
23	chr15:76914200-76928600	Weak transcription	Adipose Nuclei	Adipose
24	chr15:76915800-76924000	Weak transcription	Fetal Brain Female	brain
25	chr15:76916200-76936200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr15:76917600-76940800	Weak transcription	Right Ventricle	heart
27	chr15:76918000-76928400	Weak transcription	Stomach Smooth Muscle	stomach
28	chr15:76918200-76920800	Weak transcription	Thymus	Thymus
29	chr15:76918200-76927800	Weak transcription	Lung	lung
30	chr15:76918200-76928200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr15:76918200-76935400	Weak transcription	Primary T cells from cord blood	blood
32	chr15:76918200-76951600	Weak transcription	Brain Cingulate Gyrus	brain
33	chr15:76918400-76921000	Weak transcription	Fetal Intestine Large	intestine
34	chr15:76918400-76921400	Weak transcription	Fetal Intestine Small	intestine
35	chr15:76918400-76925400	Weak transcription	Fetal Stomach	stomach
36	chr15:76918400-76925600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr15:76918600-76926000	Weak transcription	Gastric	stomach

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