Variant report

Variant	rs4886615
Chromosome Location	chr15:75131661-75131662
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:75083424..75086045-chr15:75130919..75133658,2	K562	blood:
2	chr15:75115272..75120114-chr15:75130983..75135707,7	K562	blood:
3	chr15:75129767..75136088-chr15:75163908..75167881,8	K562	blood:
4	chr15:75073376..75079113-chr15:75130007..75137097,15	MCF-7	breast:
5	chr15:75131329..75142649-chr15:75180088..75200119,60	MCF-7	breast:

Variant related genes	Relation type
ENSG00000260824	Chromatin interaction
ENSG00000103653	Chromatin interaction
ENSG00000178802	Chromatin interaction
ENSG00000140497	Chromatin interaction
ENSG00000140506	Chromatin interaction
ENSG00000213578	Chromatin interaction
ENSG00000178761	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11072509	0.82[EUR][1000 genomes]
rs11634474	0.86[CEU][hapmap];0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs12441505	0.81[EUR][1000 genomes]
rs12442901	0.92[GIH][hapmap];0.85[MKK][hapmap]
rs1378938	0.95[GIH][hapmap]
rs1869959	0.95[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.81[YRI][hapmap];0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2168519	0.92[GIH][hapmap]
rs2290574	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2301249	0.92[GIH][hapmap];0.93[LWK][hapmap];0.84[MKK][hapmap]
rs2305668	0.85[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs3935077	0.83[EUR][1000 genomes]
rs4886406	0.81[MKK][hapmap]
rs4886613	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4886619	0.90[GIH][hapmap];0.86[LWK][hapmap];0.81[MKK][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes]
rs4886633	0.83[CEU][hapmap]
rs6495126	0.83[CEU][hapmap];0.88[GIH][hapmap]
rs6495127	0.83[CEU][hapmap];0.88[GIH][hapmap]
rs7085	0.95[GIH][hapmap];0.84[LWK][hapmap]
rs7162232	0.83[CEU][hapmap];0.92[GIH][hapmap];0.86[LWK][hapmap];0.86[MKK][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs7176022	0.83[CEU][hapmap];0.90[GIH][hapmap];0.81[LWK][hapmap];0.85[MKK][hapmap];0.82[TSI][hapmap]
rs7180432	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7180484	0.81[ASW][hapmap];0.83[CEU][hapmap];0.95[GIH][hapmap];0.95[LWK][hapmap];0.92[MKK][hapmap];0.82[TSI][hapmap];0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs7497201	0.83[CEU][hapmap];0.88[GIH][hapmap]
rs8031937	0.83[CEU][hapmap];0.88[GIH][hapmap]
rs8033381	0.92[GIH][hapmap];0.84[MKK][hapmap]
rs8042694	0.88[GIH][hapmap]
rs9210	1.00[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap]
rs936228	0.87[ASW][hapmap];0.91[CEU][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs936229	0.87[ASW][hapmap];0.91[CEU][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs936230	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap];0.82[YRI][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
3	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
4	nsv904382	chr15:75129594-75140854	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs4886615	SCAMP2	cis	parietal	SCAN
rs4886615	ENSG00000140474	cis	multi-tissue	Pritchard
rs4886615	ULK3	cis	Whole Blood	GTEx
rs4886615	MPI	cis	multi-tissue	Pritchard
rs4886615	SCAMP5	cis	cerebellum	SCAN
rs4886615	MPI	Cis_1M	lymphoblastoid	RTeQTL
rs4886615	MPI	cis	parietal	SCAN
rs4886615	MPI	cis	lymphoblastoid	seeQTL
rs4886615	ULK3	cis	multi-tissue	Pritchard
rs4886615	COX5A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75121400-75132000	Weak transcription	A549	lung
2	chr15:75121400-75134600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr15:75121800-75134600	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr15:75123800-75134200	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr15:75123800-75134200	Weak transcription	Primary B cells from cord blood	blood
6	chr15:75123800-75134400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr15:75123800-75134400	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr15:75123800-75134400	Weak transcription	HSMM	muscle
9	chr15:75124000-75134400	Weak transcription	HSMMtube	muscle
10	chr15:75124200-75132200	Weak transcription	K562	blood
11	chr15:75124400-75134400	Weak transcription	Fetal Lung	lung
12	chr15:75124800-75134400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr15:75124800-75134400	Weak transcription	Psoas Muscle	Psoas
14	chr15:75125000-75134000	Weak transcription	Stomach Mucosa	stomach
15	chr15:75125000-75134600	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr15:75125200-75134800	Weak transcription	Aorta	Aorta
17	chr15:75126200-75132800	Weak transcription	Hela-S3	cervix
18	chr15:75126200-75134400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr15:75126400-75132800	Weak transcription	Primary hematopoietic stem cells	blood
20	chr15:75126600-75134200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr15:75126600-75134400	Weak transcription	GM12878-XiMat	blood
22	chr15:75126800-75134600	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr15:75127200-75133400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr15:75127400-75132000	Strong transcription	Fetal Intestine Small	intestine
25	chr15:75127600-75132400	Strong transcription	Fetal Brain Female	brain
26	chr15:75127600-75133600	Strong transcription	Brain Germinal Matrix	brain
27	chr15:75127800-75132200	Strong transcription	Esophagus	oesophagus
28	chr15:75127800-75132800	Strong transcription	Fetal Muscle Trunk	muscle
29	chr15:75127800-75132800	Strong transcription	Right Ventricle	heart
30	chr15:75127800-75133000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr15:75127800-75133000	Strong transcription	Fetal Muscle Leg	muscle
32	chr15:75127800-75133000	Strong transcription	Pancreas	Pancrea
33	chr15:75127800-75133400	Strong transcription	Cortex derived primary cultured neurospheres	brain
34	chr15:75127800-75133800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr15:75127800-75133800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr15:75127800-75133800	Strong transcription	Fetal Stomach	stomach
37	chr15:75128000-75132200	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr15:75128000-75132400	Strong transcription	Brain Hippocampus Middle	brain
39	chr15:75128000-75132400	Strong transcription	Fetal Intestine Large	intestine
40	chr15:75128000-75132800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr15:75128000-75132800	Strong transcription	Brain Cingulate Gyrus	brain
42	chr15:75128000-75133000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr15:75128000-75133000	Strong transcription	Skeletal Muscle Male	skeletal muscle
44	chr15:75128000-75133400	Strong transcription	Primary T helper cells PMA-I stimulated	--
45	chr15:75128000-75133400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr15:75128000-75133400	Strong transcription	Brain Anterior Caudate	brain
47	chr15:75128000-75133400	Strong transcription	Gastric	stomach
48	chr15:75128000-75133400	Strong transcription	Lung	lung
49	chr15:75128000-75133400	Strong transcription	Rectal Mucosa Donor 29	rectum
50	chr15:75128000-75133400	Strong transcription	Sigmoid Colon	Sigmoid Colon

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