Variant report

Variant	rs2044157
Chromosome Location	chr15:75225808-75225809
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:75198406..75199931-chr15:75225105..75227266,2	MCF-7	breast:
2	chr15:75126487..75129177-chr15:75225564..75229328,3	K562	blood:
3	chr15:75199294..75201030-chr15:75224343..75226069,2	MCF-7	breast:
4	chr15:75184495..75186934-chr15:75223439..75225977,2	K562	blood:
5	chr15:75218199..75220881-chr15:75223418..75226005,3	MCF-7	breast:
6	chr15:75223447..75226028-chr15:75229839..75232204,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000178741	Chromatin interaction
ENSG00000178761	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs11072512	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11072513	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11072514	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1127796	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1130741	0.85[EUR][1000 genomes]
rs1133322	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1133323	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11630087	0.84[AMR][1000 genomes]
rs11630592	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11630918	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11633472	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11636892	0.84[AMR][1000 genomes]
rs11638130	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11639413	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11854704	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11856413	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11857695	0.81[EUR][1000 genomes]
rs12898539	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12899430	0.83[AMR][1000 genomes]
rs12899787	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12901190	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12902515	0.81[EUR][1000 genomes]
rs12903205	0.83[EUR][1000 genomes]
rs12903370	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12904326	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12904897	0.88[EUR][1000 genomes]
rs12907898	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12908365	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12909335	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12911254	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12912343	0.85[AMR][1000 genomes]
rs12912839	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12913293	0.84[EUR][1000 genomes]
rs12914217	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2415251	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34063670	0.85[AMR][1000 genomes]
rs34799293	0.84[AMR][1000 genomes]
rs35556055	0.84[AMR][1000 genomes]
rs35882241	0.85[AMR][1000 genomes]
rs4643278	0.81[EUR][1000 genomes]
rs4886413	0.84[AMR][1000 genomes]
rs4886632	0.83[EUR][1000 genomes]
rs4886636	0.84[EUR][1000 genomes]
rs4886639	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4886640	0.90[EUR][1000 genomes]
rs59945415	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62029167	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62029217	0.84[AMR][1000 genomes]
rs7495664	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7495739	0.84[EUR][1000 genomes]
rs7497026	0.82[EUR][1000 genomes]
rs7497393	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8025447	0.84[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	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	esv2595466	chr15:75224476-75225972	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2044157	SCAMP5	cis	Artery Tibial	GTEx
rs2044157	SCAMP2	cis	Esophagus Mucosa	GTEx

Chromatin state (count:126 , 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	chr15:75204000-75228400	Strong transcription	HUES48 Cell Line	embryonic stem cell
3	chr15:75204600-75229200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr15:75207800-75227400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr15:75212400-75229600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr15:75212600-75229200	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr15:75212800-75226000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr15:75213200-75227000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr15:75213200-75227000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr15:75213600-75227600	Weak transcription	Psoas Muscle	Psoas
11	chr15:75217400-75229400	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr15:75220200-75227400	Weak transcription	Right Ventricle	heart
13	chr15:75221400-75226000	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr15:75221400-75226000	Weak transcription	Colon Smooth Muscle	Colon
15	chr15:75221400-75229800	Weak transcription	Spleen	Spleen
16	chr15:75221600-75226000	Weak transcription	Primary T cells from cord blood	blood
17	chr15:75221600-75226000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr15:75221600-75226200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr15:75221600-75226200	Weak transcription	Small Intestine	intestine
20	chr15:75221600-75227200	Weak transcription	Brain Anterior Caudate	brain
21	chr15:75221600-75227400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr15:75221600-75227400	Weak transcription	Brain Angular Gyrus	brain
23	chr15:75221600-75228000	Weak transcription	Fetal Brain Male	brain
24	chr15:75221600-75228600	Weak transcription	Stomach Smooth Muscle	stomach
25	chr15:75221600-75229200	Weak transcription	Fetal Kidney	kidney
26	chr15:75221600-75229200	Weak transcription	HSMMtube	muscle
27	chr15:75221600-75229400	Weak transcription	Aorta	Aorta
28	chr15:75221600-75229400	Weak transcription	Ovary	ovary
29	chr15:75221600-75229600	Weak transcription	Gastric	stomach
30	chr15:75221800-75226000	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr15:75221800-75228600	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr15:75221800-75228800	Weak transcription	Fetal Brain Female	brain
33	chr15:75222000-75227000	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr15:75222000-75228200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr15:75222000-75228600	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr15:75222000-75228800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr15:75222000-75228800	Weak transcription	Primary neutrophils fromperipheralblood	blood
38	chr15:75222000-75229200	Weak transcription	NHDF-Ad	bronchial
39	chr15:75222200-75226000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr15:75222200-75227000	Weak transcription	Colonic Mucosa	Colon
41	chr15:75222200-75227400	Weak transcription	Primary B cells from cord blood	blood
42	chr15:75222200-75227600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr15:75222200-75228200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr15:75222200-75228800	Weak transcription	NHLF	lung
45	chr15:75222200-75229200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr15:75222200-75229200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr15:75222200-75229200	Weak transcription	Brain Substantia Nigra	brain
48	chr15:75222200-75229200	Weak transcription	Esophagus	oesophagus
49	chr15:75222200-75229200	Weak transcription	NH-A	brain
50	chr15:75222400-75227000	Weak transcription	Dnd41	blood

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