Variant report

Variant	rs11574012
Chromosome Location	chr12:48298295-48298296
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:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:48221119..48223794-chr12:48297710..48299941,2	MCF-7	breast:
2	chr12:48133250..48135553-chr12:48296742..48299315,2	K562	blood:
3	chr12:48146667..48149507-chr12:48298293..48300492,2	MCF-7	breast:
4	chr12:48290491..48293041-chr12:48295549..48298546,2	K562	blood:
5	chr12:48141724..48144633-chr12:48296342..48298575,2	K562	blood:
6	chr12:48167510..48169147-chr12:48296564..48298713,2	MCF-7	breast:
7	chr12:48297320..48300707-chr12:48356346..48358827,3	MCF-7	breast:
8	chr12:48296295..48301288-chr12:48356017..48360451,6	MCF-7	breast:
9	chr12:48297838..48300182-chr12:48335522..48337383,2	MCF-7	breast:
10	chr12:48211668..48213938-chr12:48298192..48300037,2	MCF-7	breast:
11	chr12:48297604..48298533-chr17:79669555..79670407,2	Hela-S3	cervix:
12	chr12:48290096..48306593-chr12:48332606..48350271,44	MCF-7	breast:
13	chr12:48296929..48299891-chr12:48498540..48500341,2	MCF-7	breast:
14	chr12:48276120..48279378-chr12:48295337..48299363,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000211584	Chromatin interaction
ENSG00000257488	Chromatin interaction
ENSG00000134291	Chromatin interaction
ENSG00000262049	Chromatin interaction
ENSG00000061273	Chromatin interaction
ENSG00000111424	Chromatin interaction
ENSG00000205537	Chromatin interaction
ENSG00000079387	Chromatin interaction
ENSG00000262814	Chromatin interaction
ENSG00000262660	Chromatin interaction
ENSG00000152556	Chromatin interaction
ENSG00000183048	Chromatin interaction
ENSG00000079337	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11168302	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs11168305	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs11574020	1.00[ASW][hapmap];0.87[LWK][hapmap];1.00[YRI][hapmap]
rs11574027	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12581281	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58379944	1.00[EUR][1000 genomes];0.90[ASN][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	nsv428589	chr12:48282920-48341192	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs11574012	LRRK2	trans	lymphoblastoid	seeQTL
rs11574012	FAM113B	cis	lymphoblastoid	seeQTL
rs11574012	PDGFD	trans	lymphoblastoid	seeQTL
rs11574012	FAM13A	trans	lymphoblastoid	seeQTL
rs11574012	ADCY6	cis	lymphoblastoid	seeQTL
rs11574012	RASSF6	trans	lymphoblastoid	seeQTL

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48293400-48298400	Enhancers	Gastric	stomach
2	chr12:48293400-48298400	Enhancers	Stomach Mucosa	stomach
3	chr12:48294200-48298800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
4	chr12:48294400-48299000	Enhancers	Spleen	Spleen
5	chr12:48296400-48298400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr12:48296600-48298400	Flanking Active TSS	Osteobl	bone
7	chr12:48296800-48298400	Enhancers	Placenta Amnion	Placenta Amnion
8	chr12:48296800-48298400	Flanking Active TSS	Hela-S3	cervix
9	chr12:48296800-48298600	Flanking Active TSS	NH-A	brain
10	chr12:48296800-48298800	Flanking Active TSS	Primary hematopoietic stem cells	blood
11	chr12:48296800-48298800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr12:48297000-48298400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr12:48297000-48298600	Flanking Active TSS	Duodenum Mucosa	Duodenum
14	chr12:48297000-48298800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr12:48297000-48298800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
16	chr12:48297000-48299600	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
17	chr12:48297200-48298400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
18	chr12:48297200-48298400	Bivalent Enhancer	Fetal Thymus	thymus
19	chr12:48297200-48298400	Enhancers	Ovary	ovary
20	chr12:48297200-48298400	Flanking Active TSS	GM12878-XiMat	blood
21	chr12:48297200-48298600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
22	chr12:48297200-48298600	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
23	chr12:48297200-48298800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
24	chr12:48297400-48298400	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr12:48297400-48298400	Bivalent Enhancer	Brain Angular Gyrus	brain
26	chr12:48297400-48298400	Bivalent Enhancer	HepG2	liver
27	chr12:48297400-48298600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr12:48297400-48298600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr12:48297400-48298600	Flanking Active TSS	Colon Smooth Muscle	Colon
30	chr12:48297600-48298400	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
31	chr12:48297600-48298400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
32	chr12:48297600-48298400	Bivalent Enhancer	Brain Cingulate Gyrus	brain
33	chr12:48297600-48298600	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
34	chr12:48297600-48298600	Flanking Active TSS	K562	blood
35	chr12:48297600-48299000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr12:48297600-48299600	Active TSS	Small Intestine	intestine
37	chr12:48297600-48299600	Flanking Active TSS	Stomach Smooth Muscle	stomach
38	chr12:48297600-48300000	Active TSS	HSMMtube	muscle
39	chr12:48297800-48298600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
40	chr12:48297800-48298600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
41	chr12:48297800-48298600	Flanking Active TSS	HUVEC	blood vessel
42	chr12:48297800-48298800	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
43	chr12:48297800-48298800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
44	chr12:48297800-48298800	Flanking Active TSS	Placenta	Placenta
45	chr12:48297800-48299000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr12:48297800-48299000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr12:48297800-48299000	Active TSS	HMEC	breast
48	chr12:48297800-48299000	Active TSS	NHDF-Ad	bronchial
49	chr12:48297800-48299000	Active TSS	NHLF	lung
50	chr12:48297800-48299400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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