Variant report

Variant	rs4886410
Chromosome Location	chr15:75065644-75065645
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:75063283..75067975-chr15:75109233..75113882,6	MCF-7	breast:
2	chr15:75064340..75065920-chr15:75077718..75079828,2	MCF-7	breast:
3	chr15:75062956..75068550-chr15:75133333..75136759,7	MCF-7	breast:
4	chr15:75065072..75069457-chr15:75091713..75095477,3	MCF-7	breast:
5	chr15:75065380..75067175-chr15:75075106..75076815,2	K562	blood:
6	chr15:75051136..75052999-chr15:75065266..75067915,2	K562	blood:
7	chr15:75063951..75065654-chr15:75182118..75184747,3	MCF-7	breast:
8	chr15:75062865..75065750-chr15:75072309..75074683,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000261606	Chromatin interaction
ENSG00000178802	Chromatin interaction
ENSG00000140474	Chromatin interaction
ENSG00000103653	Chromatin interaction
ENSG00000140506	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11072507	0.88[CHB][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11072508	0.92[CEU][hapmap];0.92[CHB][hapmap];0.86[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11630478	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11632414	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11635664	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11636952	0.96[CEU][hapmap]
rs12591513	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12594062	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12898997	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12903541	0.90[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12903896	0.90[AMR][1000 genomes]
rs12905199	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12909307	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12917376	0.94[ASN][1000 genomes]
rs1378940	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1378941	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1378942	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2168518	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2470890	0.83[CEU][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2472304	0.83[CEU][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2960192	0.92[AMR][1000 genomes]
rs34862454	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35206230	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3765066	0.83[CEU][hapmap]
rs3784789	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62006567	0.83[AMR][1000 genomes];0.88[ASN][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	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4886410	COX5A	Cis_1M	lymphoblastoid	RTeQTL
rs4886410	SCAMP5	cis	lung	GTEx
rs4886410	SCAMP5	cis	Artery Tibial	GTEx

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75055600-75065800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:75056000-75069000	Weak transcription	Lung	lung
3	chr15:75061400-75069000	Weak transcription	Liver	Liver
4	chr15:75062800-75069200	Enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr15:75063000-75066800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr15:75063200-75066800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr15:75063200-75066800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr15:75063200-75066800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr15:75063200-75067400	Enhancers	Primary B cells from cord blood	blood
10	chr15:75063200-75069400	Enhancers	Primary B cells from peripheral blood	blood
11	chr15:75063200-75069400	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr15:75063400-75067600	Weak transcription	Spleen	Spleen
13	chr15:75063400-75068000	Enhancers	Primary neutrophils fromperipheralblood	blood
14	chr15:75063400-75069400	Enhancers	Primary T cells fromperipheralblood	blood
15	chr15:75063600-75067800	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr15:75063600-75069000	Enhancers	Rectal Mucosa Donor 29	rectum
17	chr15:75063800-75067600	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr15:75063800-75069000	Weak transcription	Fetal Heart	heart
19	chr15:75063800-75069000	Weak transcription	Right Atrium	heart
20	chr15:75064000-75065800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr15:75064000-75065800	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr15:75064000-75066000	Weak transcription	NHEK	skin
23	chr15:75064000-75066200	Enhancers	Esophagus	oesophagus
24	chr15:75064000-75066400	Enhancers	Colonic Mucosa	Colon
25	chr15:75064000-75069400	Weak transcription	Fetal Brain Male	brain
26	chr15:75064200-75065800	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr15:75064200-75066000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr15:75064200-75066000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr15:75064200-75066600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
30	chr15:75064200-75067400	Weak transcription	Thymus	Thymus
31	chr15:75064400-75065800	Weak transcription	HMEC	breast
32	chr15:75064400-75066000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr15:75064400-75066200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr15:75064400-75066400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr15:75064400-75068000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr15:75064400-75069000	Weak transcription	HUVEC	blood vessel
37	chr15:75064400-75069400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr15:75064400-75069400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr15:75064400-75069400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr15:75064600-75065800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr15:75064600-75065800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr15:75064600-75065800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr15:75064600-75065800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr15:75064600-75065800	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr15:75064600-75065800	Weak transcription	Fetal Thymus	thymus
46	chr15:75064600-75065800	Weak transcription	Monocytes-CD14+_RO01746	blood
47	chr15:75064600-75066000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr15:75064600-75066000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr15:75064600-75067000	Enhancers	Brain Hippocampus Middle	brain
50	chr15:75064600-75067600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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