Variant report

Variant	rs12900662
Chromosome Location	chr15:75155662-75155663
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:75149519..75152339-chr15:75154126..75156514,3	K562	blood:
2	chr15:75155291..75158241-chr15:75246616..75248751,2	K562	blood:
3	chr15:75153777..75156294-chr15:75158618..75161224,2	K562	blood:
4	chr15:75149519..75152391-chr15:75152798..75156514,5	K562	blood:
5	chr15:75154429..75158026-chr15:75164223..75166299,3	MCF-7	breast:
6	chr15:75152352..75156342-chr15:75158618..75163297,4	K562	blood:

Variant related genes	Relation type
ENSG00000140497	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs11072511	0.95[EUR][1000 genomes]
rs11072512	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11072514	0.82[EUR][1000 genomes]
rs1127796	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1130741	0.92[EUR][1000 genomes]
rs1133322	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1133323	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11630918	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11633472	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11638130	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11854704	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11856413	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11857695	0.97[EUR][1000 genomes]
rs12898539	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12899430	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12899787	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12901190	0.80[EUR][1000 genomes]
rs12902515	0.97[EUR][1000 genomes]
rs12903205	0.96[EUR][1000 genomes]
rs12903370	0.82[EUR][1000 genomes]
rs12904326	0.81[EUR][1000 genomes]
rs12904897	0.90[EUR][1000 genomes]
rs12907898	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12908365	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12909335	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12911254	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12912839	0.82[EUR][1000 genomes]
rs12913293	0.93[EUR][1000 genomes]
rs12914217	0.85[AMR][1000 genomes]
rs4643278	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4886608	0.96[EUR][1000 genomes]
rs4886632	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4886636	0.91[EUR][1000 genomes]
rs4886639	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs59945415	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62029167	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7495664	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7495739	0.93[EUR][1000 genomes]
rs7497026	0.86[EUR][1000 genomes]
rs7497393	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8025447	0.91[EUR][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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12900662	COX5A	Cis_1M	lymphoblastoid	RTeQTL
rs12900662	SCAMP2	cis	Esophagus Mucosa	GTEx
rs12900662	SCAMP5	cis	Artery Tibial	GTEx
rs12900662	MPI	Cis_1M	lymphoblastoid	RTeQTL
rs12900662	SCAMP2	cis	Whole Blood	GTEx
rs12900662	SCAMP2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75136200-75155800	Weak transcription	NH-A	brain
2	chr15:75136200-75160000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr15:75136200-75161800	Weak transcription	Fetal Kidney	kidney
4	chr15:75136400-75158000	Weak transcription	NHDF-Ad	bronchial
5	chr15:75136600-75163000	Weak transcription	Fetal Brain Male	brain
6	chr15:75137000-75164800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr15:75143600-75163000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr15:75145000-75160000	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr15:75146000-75158200	Weak transcription	NHLF	lung
10	chr15:75146000-75164800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr15:75146200-75163200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr15:75146400-75155800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr15:75146400-75158400	Weak transcription	HUVEC	blood vessel
14	chr15:75146400-75160400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr15:75146400-75161800	Weak transcription	Fetal Lung	lung
16	chr15:75146400-75163200	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr15:75146600-75159400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr15:75146600-75159400	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr15:75146600-75160000	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr15:75146600-75163000	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr15:75146600-75164600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr15:75146800-75155800	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr15:75146800-75158600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr15:75146800-75159800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr15:75147000-75158400	Weak transcription	Liver	Liver
26	chr15:75147000-75159600	Weak transcription	Fetal Brain Female	brain
27	chr15:75147000-75160000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr15:75147000-75164800	Weak transcription	Ovary	ovary
29	chr15:75147200-75159400	Weak transcription	Thymus	Thymus
30	chr15:75147200-75164800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr15:75149800-75155800	Weak transcription	HSMM	muscle
32	chr15:75150000-75156000	Weak transcription	HSMMtube	muscle
33	chr15:75150000-75158400	Weak transcription	A549	lung
34	chr15:75150000-75158600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr15:75150000-75160000	Weak transcription	Rectal Smooth Muscle	rectum
36	chr15:75150000-75160200	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr15:75150200-75157800	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr15:75150200-75160200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr15:75150400-75159600	Weak transcription	Dnd41	blood
40	chr15:75150400-75161800	Weak transcription	Aorta	Aorta
41	chr15:75150600-75155800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr15:75150600-75155800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr15:75150600-75156000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr15:75150600-75156000	Weak transcription	Monocytes-CD14+_RO01746	blood
45	chr15:75150600-75159600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr15:75150600-75159600	Weak transcription	K562	blood
47	chr15:75150600-75160200	Weak transcription	Brain Germinal Matrix	brain
48	chr15:75150800-75155800	Weak transcription	Hela-S3	cervix
49	chr15:75151000-75155800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr15:75151000-75156800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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