Variant report

Variant	rs1200353
Chromosome Location	chr15:41836234-41836235
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:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:62609094..62609648-chr15:41836152..41836752,2	Hela-S3	cervix:
2	chr15:41827251..41831779-chr15:41832424..41837409,12	K562	blood:
3	chr15:41785172..41787151-chr15:41835585..41837884,2	MCF-7	breast:
4	chr15:41834571..41836708-chr15:41849262..41851156,2	K562	blood:
5	chr15:41835713..41840265-chr15:41851401..41853463,4	K562	blood:
6	chr15:41836113..41836929-chr9:140135486..140135990,2	HCT-116	colon:
7	chr15:41835948..41836538-chr8:17941062..17941618,2	NB4	blood:
8	chr15:41783980..41786928-chr15:41835398..41839034,5	K562	blood:
9	chr15:41784244..41787186-chr15:41835793..41838130,2	MCF-7	breast:
10	chr15:41835700..41837704-chr15:42118864..42120391,2	K562	blood:
11	chr15:41812182..41819156-chr15:41830894..41838104,9	K562	blood:
12	chr15:41407191..41409421-chr15:41835564..41837898,2	MCF-7	breast:
13	chr15:41836090..41836866-chr19:17905832..17906456,2	Hela-S3	cervix:

No data

Variant related genes	Relation type
ENSG00000188229	Chromatin interaction
ENSG00000243789	Chromatin interaction
ENSG00000104763	Chromatin interaction
ENSG00000137825	Chromatin interaction
ENSG00000103932	Chromatin interaction
ENSG00000250379	Chromatin interaction
ENSG00000168970	Chromatin interaction
ENSG00000179913	Chromatin interaction
ENSG00000128908	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000092445	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11858506	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1473781	0.86[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.89[ASN][1000 genomes]
rs2012453	0.84[ASN][1000 genomes]
rs2289743	0.91[JPT][hapmap]
rs2297379	0.86[CHB][hapmap];0.89[CHD][hapmap]
rs2297383	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2412619	0.94[ASN][1000 genomes]
rs2412620	0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2588323	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28477443	0.95[ASN][1000 genomes]
rs6493004	0.83[JPT][hapmap];0.87[MEX][hapmap]
rs6493005	0.83[JPT][hapmap];0.87[MEX][hapmap]
rs7163686	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9652441	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9944249	1.00[CHD][hapmap]

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	nsv904112	chr15:41806658-41836234	Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs1200353	JMJD7-PLA2G4B	cis	cerebellum	SCAN
rs1200353	NDUFAF1	cis	parietal	SCAN
rs1200353	RPAP1	cis	parietal	SCAN
rs1200353	SPTBN5	cis	cerebellum	SCAN
rs1200353	MAPKBP1	cis	cerebellum	SCAN
rs1200353	JMJD7-PLA2G4B	cis	parietal	SCAN
rs1200353	LTK	cis	lung	GTEx
rs1200353	C15orf23	cis	parietal	SCAN
rs1200353	RPAP1	cis	lymphoblastoid	seeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41835000-41836800	Active TSS	HUES64 Cell Line	embryonic stem cell
2	chr15:41835000-41837000	Active TSS	iPS-15b Cell Line	embryonic stem cell
3	chr15:41835000-41837000	Active TSS	iPS-20b Cell Line	embryonic stem cell
4	chr15:41835200-41836800	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr15:41835200-41836800	Active TSS	iPS-18 Cell Line	embryonic stem cell
6	chr15:41835200-41836800	Active TSS	NHLF	lung
7	chr15:41835200-41837000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr15:41835400-41836800	Active TSS	HUES48 Cell Line	embryonic stem cell
9	chr15:41835400-41836800	Active TSS	K562	blood
10	chr15:41835400-41837000	Active TSS	GM12878-XiMat	blood
11	chr15:41835400-41837000	Active TSS	HepG2	liver
12	chr15:41835600-41836400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr15:41835600-41836400	Active TSS	HMEC	breast
14	chr15:41835600-41836600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
15	chr15:41835600-41836600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr15:41835600-41836800	Active TSS	H9 Cell Line	embryonic stem cell
17	chr15:41835600-41836800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr15:41835600-41836800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr15:41835600-41836800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr15:41835600-41836800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr15:41835600-41836800	Active TSS	Muscle Satellite Cultured Cells	--
22	chr15:41835600-41836800	Active TSS	Fetal Brain Female	brain
23	chr15:41835600-41836800	Active TSS	Rectal Mucosa Donor 31	rectum
24	chr15:41835600-41836800	Active TSS	Skeletal Muscle Male	skeletal muscle
25	chr15:41835600-41836800	Active TSS	NHDF-Ad	bronchial
26	chr15:41835600-41836800	Active TSS	NHEK	skin
27	chr15:41835600-41837000	Active TSS	H1 Cell Line	embryonic stem cell
28	chr15:41835600-41837000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr15:41835600-41837000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr15:41835600-41837000	Active TSS	HUES6 Cell Line	embryonic stem cell
31	chr15:41835600-41837000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr15:41835600-41837000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr15:41835600-41837000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr15:41835600-41837000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr15:41835600-41837000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr15:41835600-41837000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr15:41835600-41837000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
38	chr15:41835600-41837000	Active TSS	A549	lung
39	chr15:41835600-41837000	Active TSS	HSMM	muscle
40	chr15:41835600-41837000	Active TSS	HSMMtube	muscle
41	chr15:41835800-41836400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
42	chr15:41835800-41836400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
43	chr15:41835800-41836400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
44	chr15:41835800-41836400	Flanking Active TSS	Fetal Brain Male	brain
45	chr15:41835800-41836400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
46	chr15:41835800-41836400	Active TSS	Small Intestine	intestine
47	chr15:41835800-41836600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
48	chr15:41835800-41836600	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
49	chr15:41835800-41836600	Active TSS	Esophagus	oesophagus
50	chr15:41835800-41836600	Active TSS	Gastric	stomach

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