Variant report

Variant	rs1378938
Chromosome Location	chr15:75096443-75096444
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:75090844..75093273-chr15:75095406..75098069,2	K562	blood:
2	chr15:75094936..75096748-chr15:75098181..75100444,2	K562	blood:
3	chr15:75094936..75097374-chr15:75098181..75101253,3	K562	blood:
4	chr15:75094317..75097312-chr15:75098901..75101095,6	MCF-7	breast:
5	chr15:75096057..75099661-chr15:75118891..75121480,3	K562	blood:

Variant related genes	Relation type
ENSG00000103653	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs11072509	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11634474	0.95[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11636952	0.83[CEU][hapmap]
rs12441505	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12442901	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1350193	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1543927	0.95[CEU][hapmap]
rs1869959	0.81[CEU][hapmap]
rs2071501	0.84[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs2168519	0.88[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap];0.90[TSI][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2301249	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2472299	0.82[CEU][hapmap]
rs3784790	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3935077	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4886406	0.95[CEU][hapmap];0.82[CHB][hapmap]
rs4886615	0.95[GIH][hapmap]
rs4886619	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4886629	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6495126	0.88[GIH][hapmap]
rs6495127	0.88[GIH][hapmap]
rs7085	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7162232	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7176022	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7180484	0.95[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72625792	0.83[ASN][1000 genomes]
rs72730503	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7497201	0.88[GIH][hapmap]
rs762551	0.82[CEU][hapmap]
rs8031937	0.88[GIH][hapmap]
rs8033381	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8042694	0.88[GIH][hapmap]
rs9210	0.86[CEU][hapmap];0.97[GIH][hapmap]
rs936226	1.00[CEU][hapmap];0.86[CHB][hapmap];0.87[EUR][1000 genomes]
rs936228	0.95[GIH][hapmap]
rs936229	0.95[GIH][hapmap]
rs936230	0.82[CEU][hapmap];0.88[GIH][hapmap]

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	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

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs1378938	SCAMP2	cis	parietal	SCAN
rs1378938	NEO1	cis	parietal	SCAN
rs1378938	SCAMP5	cis	cerebellum	SCAN
rs1378938	COX5A	Cis_1M	lymphoblastoid	RTeQTL
rs1378938	CSK	cis	lymphoblastoid	seeQTL
rs1378938	ULK3	cis	Whole Blood	GTEx
rs1378938	MPI	Cis_1M	lymphoblastoid	RTeQTL
rs1378938	MPI	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75082400-75098400	Weak transcription	Fetal Kidney	kidney
2	chr15:75086000-75107400	Weak transcription	Fetal Brain Male	brain
3	chr15:75086200-75098000	Strong transcription	Fetal Stomach	stomach
4	chr15:75087200-75100200	Weak transcription	Right Atrium	heart
5	chr15:75089400-75097600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr15:75089800-75097200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr15:75090000-75097200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr15:75090000-75097600	Strong transcription	Thymus	Thymus
9	chr15:75090000-75097800	Strong transcription	Brain Germinal Matrix	brain
10	chr15:75090200-75096800	Strong transcription	Cortex derived primary cultured neurospheres	brain
11	chr15:75090400-75096600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr15:75090400-75096600	Strong transcription	Placenta Amnion	Placenta Amnion
13	chr15:75090400-75096800	Strong transcription	Rectal Smooth Muscle	rectum
14	chr15:75090400-75097000	Strong transcription	Dnd41	blood
15	chr15:75090400-75097600	Strong transcription	Fetal Brain Female	brain
16	chr15:75090600-75097000	Strong transcription	Muscle Satellite Cultured Cells	--
17	chr15:75090600-75097600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr15:75090800-75096800	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr15:75091000-75097000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr15:75091200-75097600	Weak transcription	Psoas Muscle	Psoas
21	chr15:75091400-75097800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr15:75091800-75097800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr15:75092000-75096600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr15:75092400-75097800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr15:75092600-75096600	Strong transcription	Gastric	stomach
26	chr15:75092600-75096800	Strong transcription	H9 Cell Line	embryonic stem cell
27	chr15:75092600-75096800	Strong transcription	Brain Angular Gyrus	brain
28	chr15:75092600-75096800	Strong transcription	Brain Inferior Temporal Lobe	brain
29	chr15:75092600-75096800	Strong transcription	Brain Substantia Nigra	brain
30	chr15:75092600-75096800	Strong transcription	NHLF	lung
31	chr15:75092600-75097000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr15:75092600-75097000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr15:75092600-75097000	Strong transcription	Brain Anterior Caudate	brain
34	chr15:75092600-75097000	Strong transcription	Brain Cingulate Gyrus	brain
35	chr15:75092600-75097200	Strong transcription	Lung	lung
36	chr15:75092600-75097200	Strong transcription	Osteobl	bone
37	chr15:75092600-75097400	Strong transcription	Primary T cells from cord blood	blood
38	chr15:75092600-75097600	Strong transcription	HUES6 Cell Line	embryonic stem cell
39	chr15:75092800-75096800	Strong transcription	Pancreas	Pancrea
40	chr15:75092800-75096800	Strong transcription	Sigmoid Colon	Sigmoid Colon
41	chr15:75092800-75097000	Strong transcription	Stomach Smooth Muscle	stomach
42	chr15:75092800-75097400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr15:75092800-75097600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr15:75092800-75097600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr15:75092800-75099000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr15:75093000-75096600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr15:75093000-75096600	Strong transcription	Skeletal Muscle Male	skeletal muscle
48	chr15:75093000-75096800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr15:75093000-75096800	Strong transcription	Adipose Nuclei	Adipose
50	chr15:75093000-75096800	Strong transcription	Brain Hippocampus Middle	brain

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