Variant report

Variant	rs12914217
Chromosome Location	chr15:75209350-75209351
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11072512	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11072513	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11072514	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs1127796	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1130741	0.86[EUR][1000 genomes]
rs1133322	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1133323	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11633472	0.83[AMR][1000 genomes]
rs11638130	0.83[AMR][1000 genomes]
rs11854704	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11856413	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs11857695	0.81[EUR][1000 genomes]
rs12898539	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12899430	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12899787	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12900662	0.85[AMR][1000 genomes]
rs12901190	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs12902515	0.81[EUR][1000 genomes]
rs12903205	0.82[EUR][1000 genomes]
rs12903370	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs12904326	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs12904897	0.87[EUR][1000 genomes]
rs12907898	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12908365	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12909335	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12912839	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12913293	0.85[EUR][1000 genomes]
rs2044157	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4643278	0.87[AMR][1000 genomes]
rs4886608	0.83[EUR][1000 genomes]
rs4886632	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4886636	0.86[EUR][1000 genomes]
rs4886639	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59945415	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62029167	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7495664	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7495739	0.85[EUR][1000 genomes]
rs7497026	0.88[EUR][1000 genomes]
rs8025447	0.86[EUR][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	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
2	esv3312325	chr15:75203053-75210647	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
3	esv3312326	chr15:75203067-75210644	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12914217	SCAMP5	cis	Artery Tibial	GTEx
rs12914217	COX5A	Cis_1M	lymphoblastoid	RTeQTL
rs12914217	MPI	Cis_1M	lymphoblastoid	RTeQTL
rs12914217	SCAMP2	cis	Esophagus Mucosa	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75199600-75229400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr15:75199800-75209400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr15:75199800-75219600	Weak transcription	Aorta	Aorta
4	chr15:75200000-75209600	Weak transcription	Psoas Muscle	Psoas
5	chr15:75200000-75209800	Weak transcription	Ovary	ovary
6	chr15:75200000-75209800	Weak transcription	Small Intestine	intestine
7	chr15:75200000-75211000	Weak transcription	Fetal Kidney	kidney
8	chr15:75200000-75211600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr15:75200000-75221000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr15:75200000-75224000	Weak transcription	Stomach Mucosa	stomach
11	chr15:75200200-75209800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr15:75200200-75209800	Weak transcription	HepG2	liver
13	chr15:75200200-75209800	Weak transcription	HMEC	breast
14	chr15:75200200-75210800	Weak transcription	Fetal Brain Male	brain
15	chr15:75200200-75211000	Weak transcription	NHDF-Ad	bronchial
16	chr15:75200400-75211000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr15:75200400-75211400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr15:75200400-75211400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr15:75200400-75221200	Weak transcription	Fetal Heart	heart
20	chr15:75201000-75213000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr15:75201000-75224600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr15:75202000-75224400	Strong transcription	Fetal Muscle Trunk	muscle
23	chr15:75202200-75211800	Strong transcription	Fetal Intestine Small	intestine
24	chr15:75202200-75212000	Strong transcription	Fetal Stomach	stomach
25	chr15:75202200-75212200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr15:75202200-75224400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr15:75202600-75224800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr15:75202600-75225000	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr15:75203000-75212600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr15:75203000-75224400	Strong transcription	Fetal Muscle Leg	muscle
31	chr15:75203000-75224600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
32	chr15:75203200-75212800	Strong transcription	Primary monocytes fromperipheralblood	blood
33	chr15:75203200-75222200	Strong transcription	Left Ventricle	heart
34	chr15:75203400-75218000	Strong transcription	Skeletal Muscle Male	skeletal muscle
35	chr15:75203800-75223000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr15:75203800-75224200	Strong transcription	Duodenum Mucosa	Duodenum
37	chr15:75203800-75224400	Strong transcription	Fetal Intestine Large	intestine
38	chr15:75203800-75224600	Strong transcription	HUES64 Cell Line	embryonic stem cell
39	chr15:75204000-75211800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr15:75204000-75212600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr15:75204000-75216600	Strong transcription	Thymus	Thymus
42	chr15:75204000-75217600	Strong transcription	Lung	lung
43	chr15:75204000-75220600	Strong transcription	Rectal Mucosa Donor 29	rectum
44	chr15:75204000-75221800	Strong transcription	Skeletal Muscle Female	skeletal muscle
45	chr15:75204000-75222200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr15:75204000-75222400	Strong transcription	HUES6 Cell Line	embryonic stem cell
47	chr15:75204000-75224200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr15:75204000-75224200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr15:75204000-75224400	Strong transcription	Placenta	Placenta
50	chr15:75204000-75224600	Strong transcription	Liver	Liver

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