Variant report

Variant	rs73438569
Chromosome Location	chr15:75354486-75354487
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:75354485..75356101-chr15:75356641..75358451,2	K562	blood:
2	chr15:75352366..75354623-chr15:75356878..75359032,2	K562	blood:
3	chr15:75320352..75323234-chr15:75352354..75354868,2	K562	blood:

Variant related genes	Relation type
ENSG00000138621	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs12148355	0.82[ASN][1000 genomes]
rs12591175	0.98[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	0.86[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	0.85[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	0.86[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	0.85[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	0.80[AFR][1000 genomes];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	0.84[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	0.95[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	0.85[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	0.95[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	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs74023908	0.82[AFR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs74023935	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74023936	0.88[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	0.90[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs73438569	SCAMP5	cis	Thyroid	GTEx
rs73438569	PPCDC	cis	Adipose Subcutaneous	GTEx
rs73438569	SCAMP5	cis	Artery Tibial	GTEx
rs73438569	SCAMP5	cis	Esophagus Mucosa	GTEx

Chromatin state (count:74 , 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	chr15:75340800-75357600	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr15:75341000-75356400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr15:75341200-75357800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr15:75342000-75357200	Weak transcription	Small Intestine	intestine
7	chr15:75342200-75357600	Weak transcription	Aorta	Aorta
8	chr15:75342400-75357400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr15:75342600-75357000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr15:75342600-75357600	Weak transcription	Hela-S3	cervix
11	chr15:75342600-75364800	Weak transcription	Primary T cells from cord blood	blood
12	chr15:75342800-75357400	Weak transcription	Thymus	Thymus
13	chr15:75342800-75361600	Weak transcription	Brain Hippocampus Middle	brain
14	chr15:75343000-75354600	Weak transcription	Stomach Smooth Muscle	stomach
15	chr15:75343200-75357400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr15:75344400-75355000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr15:75346400-75361600	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr15:75347000-75356200	Weak transcription	Ovary	ovary
19	chr15:75347000-75364000	Weak transcription	Brain Substantia Nigra	brain
20	chr15:75350600-75357000	Weak transcription	Adipose Nuclei	Adipose
21	chr15:75351000-75355000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr15:75351000-75357400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr15:75351000-75358200	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr15:75351200-75354600	Weak transcription	Pancreas	Pancrea
25	chr15:75351200-75354800	Weak transcription	HepG2	liver
26	chr15:75351200-75355000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr15:75351200-75355000	Weak transcription	Fetal Heart	heart
28	chr15:75351200-75355600	Weak transcription	Fetal Muscle Leg	muscle
29	chr15:75351200-75356400	Weak transcription	Fetal Thymus	thymus
30	chr15:75351200-75356800	Weak transcription	Fetal Intestine Large	intestine
31	chr15:75351200-75357400	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr15:75351200-75357600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr15:75351200-75357800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr15:75351200-75358000	Enhancers	Primary hematopoietic stem cells short term culture	blood
35	chr15:75351200-75358000	Weak transcription	Right Ventricle	heart
36	chr15:75351200-75358000	Weak transcription	NHEK	skin
37	chr15:75351200-75358200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr15:75351400-75354600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr15:75352200-75354600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr15:75352400-75356600	Weak transcription	Fetal Intestine Small	intestine
41	chr15:75352400-75357000	Weak transcription	Fetal Stomach	stomach
42	chr15:75352400-75358000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr15:75352800-75355200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
44	chr15:75353000-75355200	Enhancers	Monocytes-CD14+_RO01746	blood
45	chr15:75353000-75355400	Enhancers	Primary monocytes fromperipheralblood	blood
46	chr15:75353000-75357000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr15:75353200-75354800	Enhancers	Primary neutrophils fromperipheralblood	blood
48	chr15:75353200-75354800	Enhancers	Osteobl	bone
49	chr15:75353400-75354800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr15:75353400-75355800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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