Variant report

Variant	rs12902515
Chromosome Location	chr15:75160998-75160999
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:75153777..75156294-chr15:75158618..75161224,2	K562	blood:
2	chr15:75160386..75162406-chr15:75181750..75183774,2	MCF-7	breast:
3	chr15:75157220..75162664-chr15:75181204..75183708,6	MCF-7	breast:
4	chr15:75158451..75161193-chr15:75161527..75164480,2	MCF-7	breast:
5	chr15:75152352..75156342-chr15:75158618..75163297,4	K562	blood:

Variant related genes	Relation type
ENSG00000178802	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs11072511	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11072512	0.93[EUR][1000 genomes]
rs11072513	0.81[EUR][1000 genomes]
rs11072514	0.84[EUR][1000 genomes]
rs1127796	0.94[EUR][1000 genomes]
rs1130741	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1133322	0.90[EUR][1000 genomes]
rs1133323	0.83[EUR][1000 genomes]
rs11630918	0.89[EUR][1000 genomes]
rs11633472	0.87[EUR][1000 genomes]
rs11638130	0.86[EUR][1000 genomes]
rs11854704	0.88[EUR][1000 genomes]
rs11856413	0.86[EUR][1000 genomes]
rs11857695	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12439641	0.83[AFR][1000 genomes]
rs12441499	0.86[AFR][1000 genomes]
rs12898539	0.85[EUR][1000 genomes]
rs12899430	0.85[EUR][1000 genomes]
rs12899787	0.90[EUR][1000 genomes]
rs12900662	0.97[EUR][1000 genomes]
rs12901190	0.83[EUR][1000 genomes]
rs12903205	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12903370	0.84[EUR][1000 genomes]
rs12904326	0.83[EUR][1000 genomes]
rs12904897	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12907898	0.92[EUR][1000 genomes]
rs12908365	0.90[EUR][1000 genomes]
rs12909335	0.83[EUR][1000 genomes]
rs12911254	0.91[EUR][1000 genomes]
rs12912839	0.84[EUR][1000 genomes]
rs12913293	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12914217	0.81[EUR][1000 genomes]
rs2044157	0.81[EUR][1000 genomes]
rs3935818	0.85[AFR][1000 genomes]
rs4643278	0.98[EUR][1000 genomes]
rs4886608	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4886632	0.98[EUR][1000 genomes]
rs4886636	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4886639	0.85[EUR][1000 genomes]
rs56671860	0.86[AFR][1000 genomes]
rs59945415	0.91[EUR][1000 genomes]
rs60494786	0.86[AFR][1000 genomes]
rs62029167	0.91[EUR][1000 genomes]
rs7179093	0.85[AFR][1000 genomes]
rs729263	0.86[AFR][1000 genomes]
rs7495664	0.84[EUR][1000 genomes]
rs7495739	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7497026	0.89[EUR][1000 genomes]
rs7497393	0.90[EUR][1000 genomes]
rs8025447	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8032473	0.81[AFR][1000 genomes]
rs9672491	0.83[AFR][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	nsv833055	chr15:74988344-75166288	Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv904381	chr15:75108636-75242155	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs12902515	SCAMP2	cis	Esophagus Mucosa	GTEx
rs12902515	MPI	Cis_1M	lymphoblastoid	RTeQTL
rs12902515	COX5A	Cis_1M	lymphoblastoid	RTeQTL
rs12902515	SCAMP2	Cis_1M	lymphoblastoid	RTeQTL
rs12902515	SCAMP2	cis	Whole Blood	GTEx
rs12902515	SCAMP5	cis	Artery Tibial	GTEx
rs12902515	ULK3	cis	Whole Blood	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75136200-75161800	Weak transcription	Fetal Kidney	kidney
2	chr15:75136600-75163000	Weak transcription	Fetal Brain Male	brain
3	chr15:75137000-75164800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr15:75143600-75163000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr15:75146000-75164800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr15:75146200-75163200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr15:75146400-75161800	Weak transcription	Fetal Lung	lung
8	chr15:75146400-75163200	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr15:75146600-75163000	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr15:75146600-75164600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr15:75147000-75164800	Weak transcription	Ovary	ovary
12	chr15:75147200-75164800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr15:75150400-75161800	Weak transcription	Aorta	Aorta
14	chr15:75151200-75161800	Weak transcription	Brain Angular Gyrus	brain
15	chr15:75151800-75161800	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr15:75152200-75162200	Weak transcription	Brain Cingulate Gyrus	brain
17	chr15:75152400-75161800	Weak transcription	Brain Hippocampus Middle	brain
18	chr15:75153600-75162200	Enhancers	Primary T helper cells fromperipheralblood	blood
19	chr15:75155000-75162000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
20	chr15:75155800-75164400	Genic enhancers	Fetal Intestine Small	intestine
21	chr15:75156000-75164800	Enhancers	Fetal Intestine Large	intestine
22	chr15:75156600-75163800	Enhancers	Stomach Mucosa	stomach
23	chr15:75156800-75163600	Enhancers	Right Ventricle	heart
24	chr15:75157000-75163000	Enhancers	Primary monocytes fromperipheralblood	blood
25	chr15:75157600-75161800	Enhancers	Colonic Mucosa	Colon
26	chr15:75157800-75162000	Enhancers	Adipose Nuclei	Adipose
27	chr15:75157800-75164600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
28	chr15:75158000-75161800	Enhancers	Fetal Heart	heart
29	chr15:75158000-75165000	Enhancers	Spleen	Spleen
30	chr15:75158200-75162200	Enhancers	HepG2	liver
31	chr15:75158200-75164600	Enhancers	Pancreas	Pancrea
32	chr15:75158200-75165000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr15:75158400-75161600	Enhancers	Psoas Muscle	Psoas
34	chr15:75158400-75164800	Enhancers	Liver	Liver
35	chr15:75158600-75162000	Genic enhancers	Fetal Muscle Leg	muscle
36	chr15:75158600-75162000	Enhancers	Right Atrium	heart
37	chr15:75158600-75163800	Enhancers	Sigmoid Colon	Sigmoid Colon
38	chr15:75158800-75161200	Strong transcription	Fetal Stomach	stomach
39	chr15:75158800-75162000	Weak transcription	NHLF	lung
40	chr15:75159000-75161400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr15:75159000-75161800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr15:75159000-75161800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr15:75159000-75161800	Weak transcription	NH-A	brain
44	chr15:75159000-75164600	Weak transcription	Osteobl	bone
45	chr15:75159200-75161400	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr15:75159200-75161800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr15:75159200-75161800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr15:75159200-75162200	Weak transcription	Pancreatic Islets	Pancreatic Islet
49	chr15:75159200-75164000	Enhancers	Small Intestine	intestine
50	chr15:75159200-75164800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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