Variant report

Variant	rs4886648
Chromosome Location	chr15:75308837-75308838
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:75307941..75311039-chr15:75492807..75495397,4	MCF-7	breast:
2	chr15:75249504..75251132-chr15:75306617..75309149,2	MCF-7	breast:
3	chr15:75286200..75292858-chr15:75303462..75309796,11	MCF-7	breast:

Variant related genes	Relation type
ENSG00000167173	Chromatin interaction
ENSG00000178718	Chromatin interaction
ENSG00000198794	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11630918	0.86[ASW][hapmap]
rs11854975	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12148488	0.85[TSI][hapmap]
rs12487	0.86[ASW][hapmap]
rs12898551	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12900072	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2290573	0.86[ASW][hapmap]
rs2304902	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2415251	0.86[ASW][hapmap]
rs34965545	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs35078352	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35116156	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35556055	0.84[MEX][hapmap]
rs3812945	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap];0.87[TSI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4886417	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4886649	0.86[ASW][hapmap]
rs4886655	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7163362	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7181261	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8028129	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
2	nsv542435	chr15:75271788-75321117	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv527237	chr15:75305040-75321262	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4886648	MPI	cis	lymphoblastoid	seeQTL
rs4886648	SCAMP5	cis	Artery Tibial	GTEx
rs4886648	CYP11A1	cis	cerebellum	SCAN
rs4886648	ULK3	cis	parietal	SCAN
rs4886648	TLE3	cis	cerebellum	SCAN
rs4886648	COX5A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75289000-75315800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:75289400-75315400	Weak transcription	Fetal Kidney	kidney
3	chr15:75290000-75309400	Weak transcription	Gastric	stomach
4	chr15:75290000-75316000	Weak transcription	Small Intestine	intestine
5	chr15:75293200-75315800	Weak transcription	Duodenum Mucosa	Duodenum
6	chr15:75294600-75312200	Weak transcription	Adipose Nuclei	Adipose
7	chr15:75294600-75315600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr15:75300400-75312200	Weak transcription	Spleen	Spleen
9	chr15:75301000-75315400	Weak transcription	Thymus	Thymus
10	chr15:75302000-75314000	Strong transcription	Fetal Intestine Small	intestine
11	chr15:75302200-75313200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr15:75302200-75313400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr15:75303600-75309800	Strong transcription	Brain Germinal Matrix	brain
14	chr15:75303600-75313800	Strong transcription	Cortex derived primary cultured neurospheres	brain
15	chr15:75303800-75309400	Strong transcription	Brain Cingulate Gyrus	brain
16	chr15:75303800-75313800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr15:75303800-75314000	Strong transcription	Fetal Brain Female	brain
18	chr15:75304000-75309400	Strong transcription	Brain Hippocampus Middle	brain
19	chr15:75304000-75309400	Strong transcription	Brain Inferior Temporal Lobe	brain
20	chr15:75304000-75315800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr15:75304000-75316000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr15:75304200-75310000	Weak transcription	Fetal Muscle Trunk	muscle
23	chr15:75304400-75313600	Strong transcription	Fetal Stomach	stomach
24	chr15:75304600-75313200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr15:75304800-75310200	Strong transcription	Brain Angular Gyrus	brain
26	chr15:75304800-75312600	Strong transcription	Brain Anterior Caudate	brain
27	chr15:75304800-75314000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr15:75305000-75315800	Weak transcription	Right Ventricle	heart
29	chr15:75305400-75309200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr15:75305600-75310800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
31	chr15:75305600-75311400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr15:75306000-75309200	Weak transcription	Brain Substantia Nigra	brain
33	chr15:75306000-75309600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr15:75306000-75312400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr15:75306200-75316000	Weak transcription	Fetal Brain Male	brain
36	chr15:75306600-75309000	Enhancers	Placenta	Placenta
37	chr15:75306600-75309400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr15:75306800-75309200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr15:75306800-75309200	Weak transcription	Fetal Intestine Large	intestine
40	chr15:75307200-75309400	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr15:75307400-75309200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr15:75307600-75309000	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr15:75307600-75310800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr15:75307800-75315800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr15:75308200-75310400	Strong transcription	Pancreatic Islets	Pancreatic Islet
46	chr15:75308200-75315800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr15:75308400-75310200	Strong transcription	HepG2	liver
48	chr15:75308600-75310200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr15:75308600-75311200	Strong transcription	H9 Cell Line	embryonic stem cell
50	chr15:75308600-75313800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain

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