Variant report

Variant	rs936228
Chromosome Location	chr15:75132164-75132165
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:75132133-75132184	K562	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

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	chr15:75132063..75136088-chr15:75165447..75167881,5	K562	blood:
5	chr15:75063457..75064044-chr15:75132063..75132629,2	K562	blood:
6	chr15:75073376..75079113-chr15:75130007..75137097,15	MCF-7	breast:
7	chr15:75131329..75142649-chr15:75180088..75200119,60	MCF-7	breast:
8	chr15:75131716..75139878-chr15:75227772..75233177,11	MCF-7	breast:

No data

Variant related genes	Relation type
ULK3	TF binding region
ENSG00000260824	Chromatin interaction
ENSG00000103653	Chromatin interaction
ENSG00000213578	Chromatin interaction
ENSG00000178761	Chromatin interaction
ENSG00000140497	Chromatin interaction
ENSG00000178802	Chromatin interaction
ENSG00000140506	Chromatin interaction
ENSG00000178741	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs11072509	0.81[EUR][1000 genomes]
rs11634474	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs12441505	0.80[EUR][1000 genomes]
rs12442901	0.92[GIH][hapmap];0.82[MKK][hapmap]
rs1378938	0.95[GIH][hapmap]
rs1869959	0.95[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2168519	0.92[GIH][hapmap]
rs2290574	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2301249	0.92[GIH][hapmap];0.89[LWK][hapmap];0.81[MKK][hapmap]
rs2305668	0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs3935077	0.82[EUR][1000 genomes]
rs4886406	0.81[MKK][hapmap]
rs4886613	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4886615	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]
rs4886619	0.90[GIH][hapmap];0.82[LWK][hapmap];0.82[TSI][hapmap];0.80[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];0.80[LWK][hapmap]
rs7162232	0.82[CEU][hapmap];0.92[GIH][hapmap];0.82[LWK][hapmap];0.84[MKK][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes]
rs7176022	0.82[CEU][hapmap];0.90[GIH][hapmap];0.82[MKK][hapmap];0.82[TSI][hapmap]
rs7180432	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7180484	0.82[CEU][hapmap];0.95[GIH][hapmap];0.91[LWK][hapmap];0.89[MKK][hapmap];0.82[TSI][hapmap];0.81[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];0.81[MKK][hapmap]
rs8042694	0.88[GIH][hapmap]
rs9210	0.87[ASW][hapmap];0.91[CEU][hapmap];0.85[CHB][hapmap];0.87[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.95[LWK][hapmap];0.94[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap]
rs936229	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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs936230	0.95[CEU][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs936228	COX5A	Cis_1M	lymphoblastoid	RTeQTL
rs936228	MPI	cis	lymphoblastoid	seeQTL
rs936228	SCAMP2	cis	parietal	SCAN
rs936228	MPI	Cis_1M	lymphoblastoid	RTeQTL
rs936228	ULK3	cis	Whole Blood	GTEx
rs936228	SCAMP5	cis	cerebellum	SCAN
rs936228	MPI	cis	parietal	SCAN

Chromatin state (count:113 , 50 per page) page: 1 2 3

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

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