Variant report

Variant	rs60017340
Chromosome Location	chr15:76535974-76535975
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:76528141..76530731-chr15:76535158..76537334,2	K562	blood:
2	chr15:76534971..76536604-chr15:76537242..76540013,2	K562	blood:
3	chr15:76534507..76537397-chr15:76543275..76544804,2	K562	blood:
4	chr15:76534719..76537651-chr15:76635013..76637728,2	K562	blood:

Variant related genes	Relation type
ENSG00000270036	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs11072576	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11072577	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11072578	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11072579	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11072583	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11072585	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11072587	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11629459	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11631690	0.81[EUR][1000 genomes]
rs11631764	0.83[EUR][1000 genomes]
rs11631874	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11633405	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11634060	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11634472	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11634796	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11636278	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11636851	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11637473	0.86[ASN][1000 genomes]
rs11637855	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12050813	0.81[ASN][1000 genomes]
rs12050896	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12443449	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs16968083	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1850722	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1875887	0.86[ASN][1000 genomes]
rs1875888	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2007928	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2016734	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2404974	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2456049	0.88[ASN][1000 genomes]
rs2456050	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2456057	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2456071	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2469548	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2938697	0.86[ASN][1000 genomes]
rs35831705	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3784449	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3898352	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3915459	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3915460	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3927264	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3958426	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3991792	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3991793	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3991794	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4592616	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4886486	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4886487	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4886488	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4886777	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4886779	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4886780	0.85[AMR][1000 genomes]
rs4886781	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4886783	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4886784	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4886787	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4886789	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4886791	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs5012144	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55805818	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56737606	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs57182285	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60290059	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60371615	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60561507	0.80[EUR][1000 genomes]
rs61018254	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61275737	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61300240	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62027018	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62027047	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62027048	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62030232	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62030246	0.80[ASN][1000 genomes]
rs6495197	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7177923	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7179750	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7180462	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8028504	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8029637	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8030454	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8033494	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8039063	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs870295	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs879625	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs883993	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs937732	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs937733	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][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	nsv569998	chr15:76232605-76550938	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	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
3	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
rs60017340	ISL2	Cis_1M	lymphoblastoid	RTeQTL
rs60017340	RP11-593F23.1	cis	Skin Sun Exposed Lower leg	GTEx
rs60017340	SCAPER	cis	lung	GTEx
rs60017340	SCAPER	Cis_1M	lymphoblastoid	RTeQTL
rs60017340	SCAPER	cis	Whole Blood	GTEx
rs60017340	SCAPER	cis	Thyroid	GTEx

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:76503600-76551400	Weak transcription	Small Intestine	intestine
2	chr15:76507200-76551400	Weak transcription	Brain Hippocampus Middle	brain
3	chr15:76508400-76546000	Weak transcription	Brain Anterior Caudate	brain
4	chr15:76510200-76555400	Weak transcription	Psoas Muscle	Psoas
5	chr15:76510400-76538000	Weak transcription	HUVEC	blood vessel
6	chr15:76510400-76538200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr15:76510400-76555000	Weak transcription	NH-A	brain
8	chr15:76513200-76559400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr15:76513800-76551400	Weak transcription	Stomach Mucosa	stomach
10	chr15:76516400-76550600	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr15:76517200-76551800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr15:76517400-76544600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr15:76517400-76549200	Weak transcription	Fetal Kidney	kidney
14	chr15:76517400-76550600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr15:76517400-76550600	Weak transcription	Pancreas	Pancrea
16	chr15:76517400-76559400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr15:76517600-76550600	Weak transcription	Aorta	Aorta
18	chr15:76517600-76550600	Weak transcription	Ovary	ovary
19	chr15:76517600-76551200	Weak transcription	Right Ventricle	heart
20	chr15:76517600-76551400	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr15:76517600-76553800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr15:76518200-76550400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr15:76518600-76538600	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr15:76521400-76551600	Weak transcription	Left Ventricle	heart
25	chr15:76522400-76554400	Weak transcription	Fetal Heart	heart
26	chr15:76523600-76537000	Weak transcription	Thymus	Thymus
27	chr15:76523600-76544600	Weak transcription	Lung	lung
28	chr15:76523600-76546200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr15:76523600-76546600	Weak transcription	Fetal Muscle Leg	muscle
30	chr15:76523600-76550600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr15:76523600-76550600	Weak transcription	Primary T helper cells PMA-I stimulated	--
32	chr15:76523600-76550600	Weak transcription	Colonic Mucosa	Colon
33	chr15:76523600-76550600	Weak transcription	Fetal Muscle Trunk	muscle
34	chr15:76523800-76551200	Weak transcription	Fetal Thymus	thymus
35	chr15:76523800-76551800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr15:76524000-76547800	Weak transcription	Duodenum Mucosa	Duodenum
37	chr15:76524000-76551600	Weak transcription	HMEC	breast
38	chr15:76524200-76542600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr15:76524200-76553000	Weak transcription	NHDF-Ad	bronchial
40	chr15:76525200-76550600	Weak transcription	Primary T cells fromperipheralblood	blood
41	chr15:76525200-76550600	Weak transcription	GM12878-XiMat	blood
42	chr15:76525600-76545400	Weak transcription	Primary T cells from cord blood	blood
43	chr15:76525600-76547600	Weak transcription	Primary hematopoietic stem cells	blood
44	chr15:76527600-76544800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr15:76527600-76550600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr15:76527600-76550600	Weak transcription	Esophagus	oesophagus
47	chr15:76529000-76546200	Weak transcription	Right Atrium	heart
48	chr15:76529000-76550600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr15:76529000-76551000	Weak transcription	K562	blood
50	chr15:76530400-76550600	Weak transcription	Fetal Stomach	stomach

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