Variant report

Variant	rs2415251
Chromosome Location	chr15:75242155-75242156
allele	C/T
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:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:75227405..75232101-chr15:75240880..75245269,7	K562	blood:
2	chr15:75062011..75065079-chr15:75241934..75244440,3	K562	blood:
3	chr15:75190211..75193395-chr15:75240493..75244229,3	K562	blood:
4	chr15:75133829..75136653-chr15:75240759..75243011,2	MCF-7	breast:
5	chr15:75241283..75245937-chr15:75246466..75251026,6	MCF-7	breast:
6	chr15:75227744..75230644-chr15:75241148..75245834,4	MCF-7	breast:
7	chr15:75230684..75233545-chr15:75240666..75243192,3	MCF-7	breast:
8	chr15:75241707..75244594-chr15:75247283..75249882,3	MCF-7	breast:
9	chr15:75052007..75054133-chr15:75241107..75244703,3	K562	blood:
10	chr15:75240908..75244606-chr15:75245585..75249293,3	K562	blood:
11	chr15:75237193..75238975-chr15:75241477..75242984,2	MCF-7	breast:
12	chr15:75196119..75200207-chr15:75241156..75244541,4	MCF-7	breast:
13	chr15:75197433..75199009-chr15:75241405..75242986,2	K562	blood:
14	chr15:75080213..75082782-chr15:75242128..75244400,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000178741	Chromatin interaction
ENSG00000140474	Chromatin interaction
ENSG00000103653	Chromatin interaction
ENSG00000264386	Chromatin interaction
ENSG00000198794	Chromatin interaction
ENSG00000178761	Chromatin interaction
ENSG00000260824	Chromatin interaction
ENSG00000178718	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 10 )

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

rs_ID	r²[population]
rs11072511	0.88[CEU][hapmap];0.83[TSI][hapmap]
rs11072512	0.92[CEU][hapmap];0.88[MEX][hapmap];0.81[MKK][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs11072513	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11072514	0.96[CEU][hapmap];0.84[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1127796	0.92[CEU][hapmap];0.88[MEX][hapmap];0.81[MKK][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs1130741	0.92[CEU][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs1133322	0.96[CEU][hapmap];0.88[MEX][hapmap];0.89[MKK][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs1133323	0.84[ASW][hapmap];0.96[CEU][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap];0.84[JPT][hapmap];0.96[MEX][hapmap];0.91[MKK][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11630087	0.87[AMR][1000 genomes]
rs11630592	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11630918	0.88[CEU][hapmap];0.87[GIH][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap];0.83[EUR][1000 genomes]
rs11633472	0.84[ASW][hapmap];0.92[CEU][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap];0.84[JPT][hapmap];0.96[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11636892	0.87[AMR][1000 genomes]
rs11638130	0.84[ASW][hapmap];0.92[CEU][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap];0.84[JPT][hapmap];0.96[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11639413	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11854704	0.96[CEU][hapmap];0.88[MEX][hapmap];0.83[MKK][hapmap];0.85[TSI][hapmap];0.80[EUR][1000 genomes]
rs11856413	0.84[ASW][hapmap];0.92[CEU][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap];0.84[JPT][hapmap];0.96[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12487	0.84[CEU][hapmap]
rs12898539	0.80[EUR][1000 genomes]
rs12899787	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12901190	0.84[ASW][hapmap];0.96[CEU][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap];0.84[JPT][hapmap];0.96[MEX][hapmap];0.91[MKK][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12903370	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12904326	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12904897	0.84[EUR][1000 genomes]
rs12907898	0.82[EUR][1000 genomes]
rs12908365	0.80[EUR][1000 genomes]
rs12909335	0.84[ASW][hapmap];0.96[CEU][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap];0.84[JPT][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12911254	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12912343	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12912839	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12913293	0.80[EUR][1000 genomes]
rs2044157	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34063670	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34307821	0.81[AMR][1000 genomes]
rs34799293	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35556055	0.85[CEU][hapmap];0.87[GIH][hapmap];0.96[MEX][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35882241	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3812945	0.86[ASW][hapmap];0.87[MEX][hapmap]
rs4886413	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4886417	0.86[ASW][hapmap]
rs4886636	0.88[CEU][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs4886639	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4886640	0.88[EUR][1000 genomes]
rs4886648	0.86[ASW][hapmap]
rs56338926	0.84[AMR][1000 genomes]
rs59945415	0.85[EUR][1000 genomes]
rs62029167	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62029217	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6495122	0.81[CEU][hapmap]
rs7495664	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7495739	0.92[CEU][hapmap];0.87[TSI][hapmap];0.80[EUR][1000 genomes]
rs7497393	0.92[CEU][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8025447	0.81[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	nsv569993	chr15:75242155-75483752	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs2415251	SCAMP2	cis	Whole Blood	GTEx
rs2415251	COX5A	Cis_1M	lymphoblastoid	RTeQTL
rs2415251	TLE3	cis	cerebellum	SCAN
rs2415251	CYP1A1	cis	cerebellum	SCAN
rs2415251	SCAMP2	Cis_1M	lymphoblastoid	RTeQTL
rs2415251	ULK3	cis	parietal	SCAN
rs2415251	MPI	cis	lymphoblastoid	seeQTL
rs2415251	SCAMP5	cis	Artery Tibial	GTEx
rs2415251	MPI	Cis_1M	lymphoblastoid	RTeQTL
rs2415251	SCAMP2	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75231000-75243200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr15:75237000-75244400	Weak transcription	Placenta	Placenta
3	chr15:75242000-75242800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr15:75242000-75242800	Enhancers	Ovary	ovary
5	chr15:75242000-75243200	Enhancers	HUES48 Cell Line	embryonic stem cell

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