Variant report

Variant	rs12144309
Chromosome Location	chr1:114315493-114315494
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chr1:114315455-114315635	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr1:114313221-114315549	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:114315143..114317661-chr1:114324442..114326870,2	MCF-7	breast:
2	chr1:114301076..114303485-chr1:114314228..114316888,3	MCF-7	breast:
3	chr1:114310854..114312625-chr1:114314961..114316732,2	MCF-7	breast:
4	chr1:114300225..114306650-chr1:114312596..114317597,9	K562	blood:

Variant related genes	Relation type
RSBN1	TF binding region
ENSG00000116793	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11102678	0.83[GIH][hapmap]
rs1146185	0.81[GIH][hapmap]
rs12117799	1.00[CEU][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12119076	0.86[ASN][1000 genomes]
rs12129076	0.86[ASN][1000 genomes]
rs1217375	0.86[GIH][hapmap]
rs1217414	0.86[GIH][hapmap]
rs1230673	0.81[GIH][hapmap]
rs1343126	1.00[JPT][hapmap]
rs13524	0.81[GIH][hapmap]
rs1624335	0.81[GIH][hapmap]
rs1743594	0.81[GIH][hapmap]
rs2040041	0.86[GIH][hapmap];0.89[MEX][hapmap]
rs2476599	0.86[GIH][hapmap]
rs2476602	0.86[GIH][hapmap]
rs2636003	0.81[GIH][hapmap]
rs2797410	0.86[ASN][1000 genomes]
rs3789597	0.84[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2752424	chr1:114189958-114712958	Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv831093	chr1:114254167-114378235	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers 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	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12144309	MAGI3	cis	cerebellum	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:114302600-114318000	Weak transcription	Spleen	Spleen
2	chr1:114302600-114321800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:114302800-114315800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:114302800-114323200	Weak transcription	Aorta	Aorta
5	chr1:114302800-114323600	Weak transcription	Psoas Muscle	Psoas
6	chr1:114302800-114326000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr1:114302800-114326200	Weak transcription	Pancreas	Pancrea
8	chr1:114302800-114326200	Weak transcription	Right Ventricle	heart
9	chr1:114303000-114315800	Weak transcription	Fetal Stomach	stomach
10	chr1:114303000-114318800	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr1:114303000-114319000	Weak transcription	Fetal Brain Male	brain
12	chr1:114303000-114319000	Weak transcription	HSMMtube	muscle
13	chr1:114303000-114323200	Weak transcription	Fetal Heart	heart
14	chr1:114303000-114326200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr1:114303200-114317200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr1:114303200-114328400	Weak transcription	A549	lung
17	chr1:114303400-114353800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr1:114304800-114320600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr1:114308200-114326600	Weak transcription	Colonic Mucosa	Colon
20	chr1:114309000-114315800	Weak transcription	Fetal Intestine Small	intestine
21	chr1:114309000-114323600	Weak transcription	Gastric	stomach
22	chr1:114309600-114353400	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr1:114310200-114319000	Weak transcription	Left Ventricle	heart
24	chr1:114310600-114317200	Weak transcription	Fetal Brain Female	brain
25	chr1:114310600-114325400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr1:114310800-114315600	Enhancers	iPS-18 Cell Line	embryonic stem cell
27	chr1:114310800-114318600	Weak transcription	HSMM	muscle
28	chr1:114310800-114319400	Weak transcription	NH-A	brain
29	chr1:114310800-114326000	Weak transcription	HMEC	breast
30	chr1:114311000-114315800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr1:114311000-114315800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr1:114311000-114316000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr1:114311000-114316000	Weak transcription	Fetal Intestine Large	intestine
34	chr1:114311000-114316200	Weak transcription	Duodenum Mucosa	Duodenum
35	chr1:114311000-114316600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr1:114311000-114316600	Weak transcription	Fetal Muscle Trunk	muscle
37	chr1:114311000-114316600	Weak transcription	Fetal Muscle Leg	muscle
38	chr1:114311000-114316600	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr1:114311000-114316600	Weak transcription	Thymus	Thymus
40	chr1:114311000-114318400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr1:114311000-114318600	Weak transcription	Hela-S3	cervix
42	chr1:114311000-114319000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr1:114311000-114319000	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr1:114311000-114319200	Weak transcription	Osteobl	bone
45	chr1:114311000-114323600	Weak transcription	Lung	lung
46	chr1:114311000-114324800	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr1:114311000-114325800	Weak transcription	Stomach Smooth Muscle	stomach
48	chr1:114311000-114326200	Weak transcription	HUVEC	blood vessel
49	chr1:114311000-114335600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr1:114311000-114336800	Weak transcription	Fetal Kidney	kidney

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