Variant report

Variant	rs12902690
Chromosome Location	chr15:75139696-75139697
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ESR1	chr15:75139629-75140368	ECC-1	luminal epithelium:	n/a	n/a
2	ESR1	chr15:75139599-75140313	ECC-1	luminal epithelium:	n/a	n/a
3	POLR2A	chr15:75139571-75139984	HepG2	liver:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:75109403..75110158-chr15:75139541..75140351,8	MCF-7	breast:
2	chr15:75109469..75110121-chr15:75139541..75140329,6	MCF-7	breast:
3	chr15:75139250..75141212-chr15:75142432..75144699,2	K562	blood:
4	chr15:75135427..75140750-chr15:75141950..75147054,10	K562	blood:
5	chr15:75131329..75142649-chr15:75180088..75200119,60	MCF-7	breast:
6	chr15:75131716..75139878-chr15:75227772..75233177,11	MCF-7	breast:

No data

Variant related genes	Relation type
ULK3	TF binding region
ENSG00000178741	Chromatin interaction
ENSG00000178802	Chromatin interaction
ENSG00000140497	Chromatin interaction
ENSG00000260824	Chromatin interaction
ENSG00000178761	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs3765066	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904380	chr15:74869438-75142761	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
2	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
3	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
4	nsv904382	chr15:75129594-75140854	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12902690	SCAMP2	cis	Whole Blood	GTEx
rs12902690	COX5A	Cis_1M	lymphoblastoid	RTeQTL
rs12902690	MPI	Cis_1M	lymphoblastoid	RTeQTL
rs12902690	SCAMP5	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75135800-75139800	Weak transcription	Small Intestine	intestine
2	chr15:75136200-75140000	Weak transcription	Ovary	ovary
3	chr15:75136200-75144200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr15:75136200-75155800	Weak transcription	NH-A	brain
5	chr15:75136200-75160000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr15:75136200-75161800	Weak transcription	Fetal Kidney	kidney
7	chr15:75136400-75139800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr15:75136400-75139800	Weak transcription	Rectal Smooth Muscle	rectum
9	chr15:75136400-75139800	Weak transcription	Right Atrium	heart
10	chr15:75136400-75139800	Weak transcription	HMEC	breast
11	chr15:75136400-75139800	Weak transcription	Osteobl	bone
12	chr15:75136400-75140000	Weak transcription	Psoas Muscle	Psoas
13	chr15:75136400-75142000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr15:75136400-75142800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr15:75136400-75145400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr15:75136400-75147200	Strong transcription	Sigmoid Colon	Sigmoid Colon
17	chr15:75136400-75149400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr15:75136400-75158000	Weak transcription	NHDF-Ad	bronchial
19	chr15:75136600-75139800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr15:75136600-75140200	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr15:75136600-75142000	Weak transcription	HSMM	muscle
22	chr15:75136600-75142600	Weak transcription	HUVEC	blood vessel
23	chr15:75136600-75145800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr15:75136600-75146200	Strong transcription	A549	lung
25	chr15:75136600-75146600	Strong transcription	Brain Angular Gyrus	brain
26	chr15:75136600-75146800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr15:75136600-75146800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr15:75136600-75147200	Strong transcription	Primary neutrophils fromperipheralblood	blood
29	chr15:75136600-75163000	Weak transcription	Fetal Brain Male	brain
30	chr15:75136800-75139800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr15:75136800-75139800	Strong transcription	Liver	Liver
32	chr15:75136800-75140000	Strong transcription	Rectal Mucosa Donor 31	rectum
33	chr15:75136800-75140200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr15:75136800-75142400	Strong transcription	Fetal Intestine Large	intestine
35	chr15:75136800-75142800	Weak transcription	K562	blood
36	chr15:75136800-75143000	Strong transcription	HepG2	liver
37	chr15:75136800-75143400	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chr15:75136800-75143800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr15:75136800-75144200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr15:75136800-75146600	Strong transcription	HUES6 Cell Line	embryonic stem cell
41	chr15:75136800-75147000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr15:75136800-75147000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr15:75136800-75147200	Strong transcription	Colonic Mucosa	Colon
44	chr15:75137000-75139800	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr15:75137000-75140000	Strong transcription	Adipose Nuclei	Adipose
46	chr15:75137000-75142400	Strong transcription	Fetal Intestine Small	intestine
47	chr15:75137000-75146400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr15:75137000-75146800	Strong transcription	Brain Germinal Matrix	brain
49	chr15:75137000-75147000	Strong transcription	Dnd41	blood
50	chr15:75137000-75147200	Strong transcription	Lung	lung

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