Variant report

Variant	rs11639413
Chromosome Location	chr15:75243294-75243295
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:22)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:22 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:75135221..75137091-chr15:75242707..75245915,3	K562	blood:
2	chr15:75135061..75138009-chr15:75242797..75244670,2	MCF-7	breast:
3	chr15:75230141..75230921-chr15:75242458..75243335,2	K562	blood:
4	chr15:75227405..75232101-chr15:75240880..75245269,7	K562	blood:
5	chr15:75062011..75065079-chr15:75241934..75244440,3	K562	blood:
6	chr15:75063121..75064065-chr15:75242418..75243333,5	K562	blood:
7	chr15:75190211..75193395-chr15:75240493..75244229,3	K562	blood:
8	chr15:75241283..75245937-chr15:75246466..75251026,6	MCF-7	breast:
9	chr15:75227744..75230644-chr15:75241148..75245834,4	MCF-7	breast:
10	chr15:75052007..75053577-chr15:75242225..75244703,2	K562	blood:
11	chr15:75061714..75065079-chr15:75242940..75246213,4	K562	blood:
12	chr15:75227405..75230380-chr15:75242647..75245130,3	K562	blood:
13	chr15:75241707..75244594-chr15:75247283..75249882,3	MCF-7	breast:
14	chr15:75052007..75054133-chr15:75241107..75244703,3	K562	blood:
15	chr15:75240908..75244606-chr15:75245585..75249293,3	K562	blood:
16	chr15:75242403..75243361-chr15:75280099..75281035,2	MCF-7	breast:
17	chr15:75062145..75062861-chr15:75242653..75243298,2	K562	blood:
18	chr15:75075073..75076597-chr15:75243005..75244574,2	MCF-7	breast:
19	chr15:75196973..75199387-chr15:75242490..75244208,2	MCF-7	breast:
20	chr15:75074287..75074820-chr15:75242442..75243401,2	K562	blood:
21	chr15:75196119..75200207-chr15:75241156..75244541,4	MCF-7	breast:
22	chr15:75080213..75082782-chr15:75242128..75244400,2	MCF-7	breast:

No data

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

Extended variants
information (count: 48 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs11072512	0.81[EUR][1000 genomes]
rs11072513	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11072514	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1127796	0.81[EUR][1000 genomes]
rs1130741	0.81[EUR][1000 genomes]
rs1133322	0.82[EUR][1000 genomes]
rs1133323	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];1.00[ASN][1000 genomes]
rs11630918	0.83[EUR][1000 genomes]
rs11633472	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11636892	0.87[AMR][1000 genomes]
rs11638130	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11854704	0.80[EUR][1000 genomes]
rs11856413	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12898539	0.80[EUR][1000 genomes]
rs12899787	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12901190	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	0.86[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]
rs2415251	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][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	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35882241	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4886413	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4886636	0.81[EUR][1000 genomes]
rs4886639	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4886640	0.88[EUR][1000 genomes]
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]
rs7495664	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7495739	0.80[EUR][1000 genomes]
rs7497393	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8025447	0.81[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	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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11639413	MPI	Cis_1M	lymphoblastoid	RTeQTL
rs11639413	SCAMP2	Cis_1M	lymphoblastoid	RTeQTL
rs11639413	SCAMP2	cis	Whole Blood	GTEx
rs11639413	SCAMP5	cis	Artery Tibial	GTEx
rs11639413	COX5A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75237000-75244400	Weak transcription	Placenta	Placenta
2	chr15:75242200-75243400	Enhancers	iPS-20b Cell Line	embryonic stem cell
3	chr15:75242200-75243600	Enhancers	H1 Cell Line	embryonic stem cell
4	chr15:75242400-75243400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr15:75242600-75243400	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr15:75242600-75243400	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr15:75242600-75243400	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr15:75242600-75243600	Enhancers	A549	lung
9	chr15:75242600-75243800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr15:75242600-75244200	Enhancers	Hela-S3	cervix
11	chr15:75242600-75244800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr15:75242800-75243400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr15:75242800-75244000	Weak transcription	HepG2	liver
14	chr15:75242800-75245800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr15:75242800-75246400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr15:75242800-75246400	Weak transcription	Fetal Heart	heart
17	chr15:75242800-75246400	Weak transcription	Fetal Intestine Small	intestine
18	chr15:75242800-75246400	Weak transcription	Ovary	ovary
19	chr15:75242800-75246400	Weak transcription	Osteobl	bone
20	chr15:75242800-75246600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr15:75242800-75246600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr15:75242800-75247200	Weak transcription	Brain Angular Gyrus	brain
23	chr15:75242800-75247600	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr15:75242800-75248000	Weak transcription	Liver	Liver
25	chr15:75243000-75244400	Weak transcription	K562	blood
26	chr15:75243000-75246600	Weak transcription	Stomach Mucosa	stomach
27	chr15:75243000-75246800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr15:75243000-75247800	Weak transcription	Brain Anterior Caudate	brain
29	chr15:75243000-75248200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr15:75243000-75248200	Weak transcription	HMEC	breast
31	chr15:75243200-75243400	Enhancers	HUES6 Cell Line	embryonic stem cell
32	chr15:75243200-75243400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
33	chr15:75243200-75243400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr15:75243200-75243600	Enhancers	ES-I3 Cell Line	embryonic stem cell
35	chr15:75243200-75243600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr15:75243200-75246200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr15:75243200-75246200	Weak transcription	Fetal Lung	lung
38	chr15:75243200-75246400	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr15:75243200-75246400	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr15:75243200-75247200	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr15:75243200-75248000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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