Variant report

Variant	rs62030246
Chromosome Location	chr15:76553588-76553589
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 81 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs11072576	0.92[AFR][1000 genomes]
rs11072577	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11072578	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11072579	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11072583	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11072585	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11072587	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11629459	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11631874	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11633405	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11634060	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11634472	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11634796	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11636278	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11636851	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11637855	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12050896	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12443449	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16968083	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1850722	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2016734	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2404974	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2456057	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2456071	0.86[ASN][1000 genomes]
rs2469210	0.86[ASN][1000 genomes]
rs2469548	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2938697	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35831705	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3784449	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3898352	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3915459	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3915460	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3927264	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3958426	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3991792	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3991793	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3991794	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4592616	0.82[EUR][1000 genomes]
rs4886486	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4886487	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4886488	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4886779	0.81[AMR][1000 genomes]
rs4886781	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4886783	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4886784	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4886787	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4886789	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4886791	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5012144	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55794488	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55805818	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56737606	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57182285	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs60017340	0.80[ASN][1000 genomes]
rs60290059	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60371615	0.92[AFR][1000 genomes]
rs60561507	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61018254	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61275737	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61300240	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62027018	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62027047	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62027048	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62030232	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62030245	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6495197	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7177923	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7179750	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7180462	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8028504	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8029637	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8030454	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8033494	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8039063	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs870295	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs879625	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs883993	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs937732	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs937733	0.81[EUR][1000 genomes];0.83[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	nsv833057	chr15:76367848-76585868	ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv527608	chr15:76530267-76562738	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs62030246	SCAPER	cis	Thyroid	GTEx
rs62030246	SCAPER	Cis_1M	lymphoblastoid	RTeQTL
rs62030246	SCAPER	cis	lung	GTEx
rs62030246	RP11-593F23.1	cis	Skin Sun Exposed Lower leg	GTEx
rs62030246	SCAPER	cis	Whole Blood	GTEx
rs62030246	ISL2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:76510200-76555400	Weak transcription	Psoas Muscle	Psoas
2	chr15:76510400-76555000	Weak transcription	NH-A	brain
3	chr15:76513200-76559400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr15:76517400-76559400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr15:76517600-76553800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr15:76522400-76554400	Weak transcription	Fetal Heart	heart
7	chr15:76535600-76555200	Weak transcription	Brain Substantia Nigra	brain
8	chr15:76539000-76555600	Weak transcription	HUVEC	blood vessel
9	chr15:76545400-76555400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr15:76546200-76553600	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr15:76546200-76554800	Strong transcription	Hela-S3	cervix
12	chr15:76546200-76555200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr15:76546200-76556000	Strong transcription	A549	lung
14	chr15:76546800-76554200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr15:76546800-76558200	Weak transcription	Brain Angular Gyrus	brain
16	chr15:76547000-76554600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr15:76548000-76555000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr15:76549000-76555200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr15:76549400-76554600	Strong transcription	Duodenum Smooth Muscle	Duodenum
20	chr15:76549400-76555200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr15:76549600-76555000	Weak transcription	Fetal Kidney	kidney
22	chr15:76550000-76553600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr15:76550400-76554200	Strong transcription	Fetal Lung	lung
24	chr15:76550400-76563000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr15:76550600-76553800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr15:76550600-76553800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr15:76550600-76553800	Strong transcription	Rectal Mucosa Donor 31	rectum
28	chr15:76550600-76554000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr15:76550600-76554000	Strong transcription	Aorta	Aorta
30	chr15:76550600-76554000	Strong transcription	Brain Anterior Caudate	brain
31	chr15:76550600-76554000	Strong transcription	Colonic Mucosa	Colon
32	chr15:76550600-76554000	Strong transcription	Gastric	stomach
33	chr15:76550600-76554000	Strong transcription	Sigmoid Colon	Sigmoid Colon
34	chr15:76550600-76554200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr15:76550600-76554200	ZNF genes & repeats	Lung	lung
36	chr15:76550600-76554200	Strong transcription	Pancreas	Pancrea
37	chr15:76550600-76554400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr15:76550600-76554400	Strong transcription	Primary T cells fromperipheralblood	blood
39	chr15:76550600-76554600	Strong transcription	H1 Cell Line	embryonic stem cell
40	chr15:76550600-76554600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr15:76550600-76554600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr15:76550600-76554600	Strong transcription	Ovary	ovary
43	chr15:76550600-76554800	Strong transcription	Primary T helper cells fromperipheralblood	blood
44	chr15:76550600-76555000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr15:76550600-76555200	Strong transcription	Adipose Nuclei	Adipose
46	chr15:76550600-76555200	Strong transcription	HSMM	muscle
47	chr15:76550600-76555400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr15:76550600-76555400	Strong transcription	Primary T helper cells PMA-I stimulated	--
49	chr15:76550600-76555400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr15:76550600-76555400	Strong transcription	Rectal Mucosa Donor 29	rectum

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