Variant report

Variant	rs2290572
Chromosome Location	chr15:75130573-75130574
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:75129767..75136088-chr15:75163908..75167881,8	K562	blood:
2	chr15:75129762..75131472-chr15:75249225..75252165,2	K562	blood:
3	chr15:75073376..75079113-chr15:75130007..75137097,15	MCF-7	breast:
4	chr15:75127539..75130871-chr15:75182053..75185205,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000103653	Chromatin interaction
ENSG00000178802	Chromatin interaction
ENSG00000178718	Chromatin interaction
ENSG00000140497	Chromatin interaction
ENSG00000198794	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs12487	0.82[CEU][hapmap]
rs12898397	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12908814	0.96[CEU][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs936227	0.96[CEU][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2290572	SCAMP2	cis	Whole Blood	GTEx
rs2290572	COX5A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75121400-75132000	Weak transcription	A549	lung
2	chr15:75121400-75134600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr15:75121800-75134600	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr15:75122600-75131200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr15:75123200-75130600	Weak transcription	Osteobl	bone
6	chr15:75123800-75134200	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr15:75123800-75134200	Weak transcription	Primary B cells from cord blood	blood
8	chr15:75123800-75134400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr15:75123800-75134400	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr15:75123800-75134400	Weak transcription	HSMM	muscle
11	chr15:75124000-75134400	Weak transcription	HSMMtube	muscle
12	chr15:75124200-75132200	Weak transcription	K562	blood
13	chr15:75124400-75134400	Weak transcription	Fetal Lung	lung
14	chr15:75124800-75134400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr15:75124800-75134400	Weak transcription	Psoas Muscle	Psoas
16	chr15:75125000-75134000	Weak transcription	Stomach Mucosa	stomach
17	chr15:75125000-75134600	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr15:75125200-75134800	Weak transcription	Aorta	Aorta
19	chr15:75126200-75132800	Weak transcription	Hela-S3	cervix
20	chr15:75126200-75134400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr15:75126400-75132800	Weak transcription	Primary hematopoietic stem cells	blood
22	chr15:75126600-75134200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr15:75126600-75134400	Weak transcription	GM12878-XiMat	blood
24	chr15:75126800-75134600	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr15:75127200-75133400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr15:75127400-75132000	Strong transcription	Fetal Intestine Small	intestine
27	chr15:75127600-75131200	Strong transcription	Skeletal Muscle Female	skeletal muscle
28	chr15:75127600-75132400	Strong transcription	Fetal Brain Female	brain
29	chr15:75127600-75133600	Strong transcription	Brain Germinal Matrix	brain
30	chr15:75127800-75131000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr15:75127800-75132200	Strong transcription	Esophagus	oesophagus
32	chr15:75127800-75132800	Strong transcription	Fetal Muscle Trunk	muscle
33	chr15:75127800-75132800	Strong transcription	Right Ventricle	heart
34	chr15:75127800-75133000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr15:75127800-75133000	Strong transcription	Fetal Muscle Leg	muscle
36	chr15:75127800-75133000	Strong transcription	Pancreas	Pancrea
37	chr15:75127800-75133400	Strong transcription	Cortex derived primary cultured neurospheres	brain
38	chr15:75127800-75133800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr15:75127800-75133800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr15:75127800-75133800	Strong transcription	Fetal Stomach	stomach
41	chr15:75128000-75130800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr15:75128000-75131400	Strong transcription	Brain Inferior Temporal Lobe	brain
43	chr15:75128000-75132200	Strong transcription	Monocytes-CD14+_RO01746	blood
44	chr15:75128000-75132400	Strong transcription	Brain Hippocampus Middle	brain
45	chr15:75128000-75132400	Strong transcription	Fetal Intestine Large	intestine
46	chr15:75128000-75132800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr15:75128000-75132800	Strong transcription	Brain Cingulate Gyrus	brain
48	chr15:75128000-75133000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr15:75128000-75133000	Strong transcription	Skeletal Muscle Male	skeletal muscle
50	chr15:75128000-75133400	Strong transcription	Primary T helper cells PMA-I stimulated	--

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