Variant report

Variant	rs12899787
Chromosome Location	chr15:75231309-75231310
allele	A/C
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:21)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:21 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:75180806..75183670-chr15:75227670..75231591,7	K562	blood:
2	chr15:75186057..75188212-chr15:75229416..75232067,2	MCF-7	breast:
3	chr15:75230618..75232624-chr15:75232733..75234385,2	MCF-7	breast:
4	chr15:74906651..74909310-chr15:75228343..75231322,3	K562	blood:
5	chr15:75180371..75182934-chr15:75228872..75231935,3	MCF-7	breast:
6	chr15:75073739..75076026-chr15:75228940..75231737,2	MCF-7	breast:
7	chr15:75226056..75232063-chr15:75248745..75252832,9	MCF-7	breast:
8	chr15:75196219..75200292-chr15:75228985..75231952,6	MCF-7	breast:
9	chr15:75228700..75232954-chr15:75245461..75250546,13	K562	blood:
10	chr15:75230684..75233545-chr15:75240666..75243192,3	MCF-7	breast:
11	chr15:75196237..75205947-chr15:75227299..75233104,18	K562	blood:
12	chr15:75092442..75093966-chr15:75229581..75231570,2	MCF-7	breast:
13	chr15:75090885..75095958-chr15:75228068..75231576,5	K562	blood:
14	chr15:75229527..75231750-chr3:9834777..9836325,2	MCF-7	breast:
15	chr15:75164087..75166934-chr15:75231090..75233068,2	K562	blood:
16	chr15:75196272..75199556-chr15:75229911..75232060,4	MCF-7	breast:
17	chr15:75133406..75136691-chr15:75228046..75231533,6	MCF-7	breast:
18	chr15:75226664..75233309-chr15:75245862..75252227,16	K562	blood:
19	chr15:75116807..75119405-chr15:75229123..75231541,2	K562	blood:
20	chr15:75191256..75201000-chr15:75228549..75233626,13	K562	blood:
21	chr15:75131716..75139878-chr15:75227772..75233177,11	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000178761	Chromatin interaction
ENSG00000241553	Chromatin interaction
ENSG00000260919	Chromatin interaction
ENSG00000198794	Chromatin interaction
ENSG00000250151	Chromatin interaction
ENSG00000260824	Chromatin interaction
ENSG00000179335	Chromatin interaction
ENSG00000178802	Chromatin interaction
ENSG00000178718	Chromatin interaction
ENSG00000213578	Chromatin interaction
ENSG00000103653	Chromatin interaction
ENSG00000140474	Chromatin interaction
ENSG00000140497	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs11072511	0.88[EUR][1000 genomes]
rs11072512	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11072513	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11072514	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1127796	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1130741	0.94[EUR][1000 genomes]
rs1133322	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1133323	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11630592	0.81[EUR][1000 genomes]
rs11633472	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11638130	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11639413	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11854704	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11856413	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11857695	0.90[EUR][1000 genomes]
rs12898539	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12899430	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12900662	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12901190	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12902515	0.90[EUR][1000 genomes]
rs12903205	0.92[EUR][1000 genomes]
rs12903370	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12904326	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12904897	0.98[EUR][1000 genomes]
rs12907898	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12908365	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12909335	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12911254	0.82[EUR][1000 genomes]
rs12912839	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12913293	0.93[EUR][1000 genomes]
rs12914217	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2044157	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2415251	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4643278	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4886608	0.89[EUR][1000 genomes]
rs4886632	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4886636	0.94[EUR][1000 genomes]
rs4886639	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4886640	0.84[EUR][1000 genomes]
rs59945415	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62029167	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7495664	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7495739	0.93[EUR][1000 genomes]
rs7497026	0.92[EUR][1000 genomes]
rs7497393	0.83[EUR][1000 genomes]
rs8025447	0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12899787	COX5A	Cis_1M	lymphoblastoid	RTeQTL
rs12899787	SCAMP5	cis	Artery Tibial	GTEx
rs12899787	SCAMP2	cis	Esophagus Mucosa	GTEx
rs12899787	SCAMP2	cis	Whole Blood	GTEx
rs12899787	SCAMP2	Cis_1M	lymphoblastoid	RTeQTL
rs12899787	MPI	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75228600-75231600	Active TSS	A549	lung
2	chr15:75229600-75231800	Active TSS	Primary T helper naive cells from peripheral blood	blood
3	chr15:75230600-75232200	Enhancers	HepG2	liver
4	chr15:75231000-75231400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr15:75231000-75231600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr15:75231000-75233600	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr15:75231000-75243200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr15:75231200-75231800	Weak transcription	Colonic Mucosa	Colon
9	chr15:75231200-75231800	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr15:75231200-75232000	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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