Variant report

Variant	rs12106869
Chromosome Location	chr3:119314963-119314964
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:21)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:21 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAFF	chr3:119314885-119315219	K562	blood:	n/a	n/a
2	MTA3	chr3:119314705-119315717	GM12878	blood:	n/a	n/a
3	TCF12	chr3:119314884-119315161	GM12878	blood:	n/a	n/a
4	MYC	chr3:119314878-119315201	K562	blood:	n/a	n/a
5	RUNX3	chr3:119314839-119315660	GM12878	blood:	n/a	n/a
6	RCOR1	chr3:119314889-119315248	K562	blood:	n/a	n/a
7	POLR2A	chr3:119314786-119315732	GM12892	blood:	n/a	n/a
8	IRF1	chr3:119314883-119315077	K562	blood:	n/a	n/a
9	PML	chr3:119314495-119320501	GM12878	blood:	n/a	n/a
10	NFIC	chr3:119314902-119315655	GM12878	blood:	n/a	n/a
11	BHLHE40	chr3:119314957-119315629	GM12878	blood:	n/a	n/a
12	MAFK	chr3:119314882-119315215	K562	blood:	n/a	n/a
13	JUND	chr3:119314874-119315183	K562	blood:	n/a	n/a
14	EBF1	chr3:119314936-119315118	GM12878	blood:	n/a	n/a
15	ZNF143	chr3:119314861-119315475	GM12878	blood:	n/a	n/a
16	WRNIP1	chr3:119314798-119315188	GM12878	blood:	n/a	n/a
17	POLR2A	chr3:119314781-119315682	GM12891	blood:	n/a	n/a
18	EBF1	chr3:119314713-119315143	GM12878	blood:	n/a	n/a
19	POLR2A	chr3:119314772-119320568	GM12878	blood:	n/a	n/a
20	TBP	chr3:119314893-119315563	GM12878	blood:	n/a	n/a
21	FOXM1	chr3:119314957-119315720	GM12878	blood:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:119314543..119316146-chr3:119316320..119318446,2	K562	blood:
2	chr3:119310790..119313134-chr3:119314484..119316186,2	K562	blood:

No data

Variant related genes	Relation type
PLA1A	TF binding region
ENSG00000144837	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11915800	1.00[EUR][1000 genomes]
rs11918611	1.00[EUR][1000 genomes]
rs11919422	1.00[EUR][1000 genomes]
rs11927159	1.00[EUR][1000 genomes]
rs11927863	1.00[EUR][1000 genomes]
rs12106815	1.00[EUR][1000 genomes]
rs13317715	1.00[EUR][1000 genomes]
rs16830032	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58318736	1.00[EUR][1000 genomes]
rs61575899	1.00[EUR][1000 genomes]
rs6767853	1.00[EUR][1000 genomes]
rs72968486	1.00[EUR][1000 genomes]
rs73854857	1.00[EUR][1000 genomes]
rs73857025	1.00[EUR][1000 genomes]
rs7611869	1.00[EUR][1000 genomes]
rs9821005	1.00[EUR][1000 genomes]
rs9860332	1.00[EUR][1000 genomes]
rs9861284	1.00[EUR][1000 genomes]
rs9861344	1.00[EUR][1000 genomes]
rs9866191	1.00[EUR][1000 genomes]
rs9876397	1.00[EUR][1000 genomes]
rs9876408	1.00[EUR][1000 genomes]
rs9876504	1.00[EUR][1000 genomes]
rs9881550	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv829695	chr3:119178890-119367996	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv1831824	chr3:119263607-119402474	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv3963	chr3:119301064-119345904	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119299200-119315000	Weak transcription	Gastric	stomach
2	chr3:119299800-119318000	Weak transcription	Fetal Heart	heart
3	chr3:119306000-119316800	Weak transcription	Pancreas	Pancrea
4	chr3:119307600-119316400	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr3:119310600-119319800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr3:119311000-119315000	Weak transcription	Spleen	Spleen
7	chr3:119311000-119317600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr3:119311200-119316800	Weak transcription	Fetal Lung	lung
9	chr3:119314200-119315400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
10	chr3:119314200-119315600	Enhancers	Right Ventricle	heart
11	chr3:119314200-119315600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
12	chr3:119314200-119317200	Enhancers	Lung	lung
13	chr3:119314400-119315000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
14	chr3:119314400-119315000	Flanking Active TSS	HSMM	muscle
15	chr3:119314400-119315200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr3:119314400-119315200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr3:119314400-119315200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
18	chr3:119314400-119315200	Flanking Active TSS	HSMMtube	muscle
19	chr3:119314400-119315400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr3:119314400-119315600	Flanking Active TSS	Brain Hippocampus Middle	brain
21	chr3:119314400-119318600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr3:119314600-119315000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr3:119314600-119315000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr3:119314600-119315000	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr3:119314600-119315000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr3:119314600-119315000	Flanking Active TSS	Adipose Nuclei	Adipose
27	chr3:119314600-119315000	Flanking Active TSS	Liver	Liver
28	chr3:119314600-119315000	Enhancers	Brain Germinal Matrix	brain
29	chr3:119314600-119315000	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
30	chr3:119314600-119315000	Active TSS	Colonic Mucosa	Colon
31	chr3:119314600-119315000	Enhancers	Fetal Muscle Trunk	muscle
32	chr3:119314600-119315000	Flanking Active TSS	Left Ventricle	heart
33	chr3:119314600-119315000	Flanking Active TSS	Psoas Muscle	Psoas
34	chr3:119314600-119315000	Active TSS	Rectal Mucosa Donor 29	rectum
35	chr3:119314600-119315000	Flanking Active TSS	Right Atrium	heart
36	chr3:119314600-119315000	Active TSS	NHLF	lung
37	chr3:119314600-119315000	Flanking Active TSS	Osteobl	bone
38	chr3:119314600-119315200	Flanking Active TSS	Colon Smooth Muscle	Colon
39	chr3:119314600-119315200	Active TSS	Duodenum Smooth Muscle	Duodenum
40	chr3:119314600-119315200	Enhancers	Fetal Thymus	thymus
41	chr3:119314600-119315400	Flanking Active TSS	Brain Substantia Nigra	brain
42	chr3:119314600-119315400	Flanking Active TSS	GM12878-XiMat	blood
43	chr3:119314600-119315600	Enhancers	Primary hematopoietic stem cells	blood
44	chr3:119314600-119315600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr3:119314600-119315600	Active TSS	Rectal Smooth Muscle	rectum
46	chr3:119314600-119315600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
47	chr3:119314600-119316200	Enhancers	Primary hematopoietic stem cells short term culture	blood
48	chr3:119314600-119316400	Enhancers	Primary monocytes fromperipheralblood	blood
49	chr3:119314800-119315000	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr3:119314800-119315000	Active TSS	Brain Anterior Caudate	brain

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