Variant report

Variant	rs74023935
Chromosome Location	chr15:75359184-75359185
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:75339319..75341137-chr15:75356875..75359232,2	K562	blood:
2	chr15:75351256..75353866-chr15:75357532..75359933,2	K562	blood:
3	chr15:75358652..75359351-chr15:75496592..75497218,2	K562	blood:

Extended variants
information (count: 55 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs12148355	0.82[ASN][1000 genomes]
rs12591175	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12591994	0.83[ASN][1000 genomes]
rs12592477	0.80[ASN][1000 genomes]
rs12594117	0.84[AFR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2289582	0.82[ASN][1000 genomes]
rs2304904	0.83[ASN][1000 genomes]
rs28394281	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3812943	0.83[ASN][1000 genomes]
rs3816261	0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3910748	0.84[AFR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56970592	0.81[EUR][1000 genomes]
rs58294763	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58645417	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59094290	0.81[ASN][1000 genomes]
rs59303424	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61166993	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6495135	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6495136	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6495137	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6495138	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6495140	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6495142	0.82[AFR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6495146	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6495148	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7166105	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7167415	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7172989	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7173218	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7174129	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7177109	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7181942	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7182286	0.81[ASN][1000 genomes]
rs72475969	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7342591	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7342601	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73432941	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73436579	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73438537	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73438554	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73438569	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74023908	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs74023936	0.90[AFR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8024931	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8033125	0.97[ASN][1000 genomes]
rs8034149	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8036573	0.81[ASN][1000 genomes]
rs8038365	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8039433	0.89[AFR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9672996	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9673012	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9788648	0.84[EUR][1000 genomes];0.81[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	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	nsv457205	chr15:75336729-75447773	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv569994	chr15:75336729-75447773	Genic enhancers Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs74023935	SCAMP5	cis	Artery Tibial	GTEx
rs74023935	PPCDC	cis	Adipose Subcutaneous	GTEx
rs74023935	SCAMP5	cis	lung	GTEx
rs74023935	SCAMP5	cis	Thyroid	GTEx
rs74023935	SCAMP5	cis	Esophagus Mucosa	GTEx

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75340000-75360600	Weak transcription	Gastric	stomach
2	chr15:75340200-75359400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr15:75342600-75364800	Weak transcription	Primary T cells from cord blood	blood
4	chr15:75342800-75361600	Weak transcription	Brain Hippocampus Middle	brain
5	chr15:75346400-75361600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr15:75347000-75364000	Weak transcription	Brain Substantia Nigra	brain
7	chr15:75356600-75360000	Enhancers	HSMMtube	muscle
8	chr15:75356600-75360200	Enhancers	Osteobl	bone
9	chr15:75356800-75360200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr15:75356800-75361000	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr15:75356800-75366600	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr15:75357000-75359200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr15:75357000-75359400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr15:75357000-75360600	Weak transcription	Spleen	Spleen
15	chr15:75357000-75363200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr15:75357000-75365400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr15:75357200-75359800	Enhancers	Ovary	ovary
18	chr15:75357200-75360200	Enhancers	HMEC	breast
19	chr15:75357200-75360200	Enhancers	HSMM	muscle
20	chr15:75357400-75360200	Enhancers	K562	blood
21	chr15:75357400-75360800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr15:75357400-75362200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
23	chr15:75357600-75359800	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr15:75357600-75360000	Enhancers	Primary T helper cells fromperipheralblood	blood
25	chr15:75357600-75360200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr15:75357600-75360200	Enhancers	Hela-S3	cervix
27	chr15:75357600-75360800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr15:75357600-75360800	Enhancers	Primary T cells fromperipheralblood	blood
29	chr15:75357600-75361000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
30	chr15:75357600-75361000	Enhancers	Primary T killer memory cells from peripheral blood	blood
31	chr15:75357600-75361800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
32	chr15:75357600-75363200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
33	chr15:75357800-75359800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr15:75357800-75360000	Enhancers	Primary T helper cells PMA-I stimulated	--
35	chr15:75357800-75360200	Enhancers	Primary T helper naive cells from peripheral blood	blood
36	chr15:75358000-75359600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr15:75358000-75360200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
38	chr15:75358000-75360400	Enhancers	NHEK	skin
39	chr15:75358200-75360000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr15:75358200-75360200	Enhancers	Muscle Satellite Cultured Cells	--
41	chr15:75358400-75359400	Weak transcription	Left Ventricle	heart
42	chr15:75358400-75359600	Weak transcription	Right Atrium	heart
43	chr15:75358400-75361600	Weak transcription	Adipose Nuclei	Adipose
44	chr15:75358400-75361600	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr15:75358400-75361800	Weak transcription	Right Ventricle	heart
46	chr15:75358400-75368600	Weak transcription	Aorta	Aorta
47	chr15:75358600-75360800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr15:75358600-75361600	Weak transcription	Lung	lung
49	chr15:75358800-75359600	Flanking Active TSS	GM12878-XiMat	blood
50	chr15:75358800-75360200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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