Variant report

Variant	rs12117799
Chromosome Location	chr1:114318604-114318605
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:114310377..114313122-chr1:114318534..114321051,2	MCF-7	breast:
2	chr1:114317877..114322132-chr1:114322334..114326038,5	K562	blood:
3	chr1:114318179..114320042-chr1:114335877..114339119,3	K562	blood:
4	chr1:114301792..114303371-chr1:114318002..114320468,2	K562	blood:
5	chr1:114317443..114319030-chr1:114354000..114355805,2	MCF-7	breast:
6	chr1:114317996..114324872-chr1:114329159..114335059,8	K562	blood:
7	chr1:114302807..114305155-chr1:114318148..114320872,2	K562	blood:
8	chr1:114318384..114320643-chr1:114337439..114339528,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000231128	Chromatin interaction
ENSG00000116793	Chromatin interaction
ENSG00000081019	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11102660	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11588901	1.00[ASN][1000 genomes]
rs12144309	1.00[CEU][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61819372	1.00[ASN][1000 genomes]
rs61819425	1.00[ASN][1000 genomes]
rs72650671	1.00[ASN][1000 genomes]
rs72687967	1.00[ASN][1000 genomes]
rs7515189	0.86[MEX][hapmap];1.00[ASN][1000 genomes]

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
rs12117799	MAGI3	cis	cerebellum	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:114302600-114321800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:114302800-114323200	Weak transcription	Aorta	Aorta
3	chr1:114302800-114323600	Weak transcription	Psoas Muscle	Psoas
4	chr1:114302800-114326000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr1:114302800-114326200	Weak transcription	Pancreas	Pancrea
6	chr1:114302800-114326200	Weak transcription	Right Ventricle	heart
7	chr1:114303000-114318800	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr1:114303000-114319000	Weak transcription	Fetal Brain Male	brain
9	chr1:114303000-114319000	Weak transcription	HSMMtube	muscle
10	chr1:114303000-114323200	Weak transcription	Fetal Heart	heart
11	chr1:114303000-114326200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr1:114303200-114328400	Weak transcription	A549	lung
13	chr1:114303400-114353800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:114304800-114320600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr1:114308200-114326600	Weak transcription	Colonic Mucosa	Colon
16	chr1:114309000-114323600	Weak transcription	Gastric	stomach
17	chr1:114309600-114353400	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr1:114310200-114319000	Weak transcription	Left Ventricle	heart
19	chr1:114310600-114325400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr1:114310800-114319400	Weak transcription	NH-A	brain
21	chr1:114310800-114326000	Weak transcription	HMEC	breast
22	chr1:114311000-114319000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr1:114311000-114319000	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr1:114311000-114319200	Weak transcription	Osteobl	bone
25	chr1:114311000-114323600	Weak transcription	Lung	lung
26	chr1:114311000-114324800	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr1:114311000-114325800	Weak transcription	Stomach Smooth Muscle	stomach
28	chr1:114311000-114326200	Weak transcription	HUVEC	blood vessel
29	chr1:114311000-114335600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr1:114311000-114336800	Weak transcription	Fetal Kidney	kidney
31	chr1:114311000-114341800	Weak transcription	Esophagus	oesophagus
32	chr1:114311200-114319000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr1:114311200-114325800	Weak transcription	NHEK	skin
34	chr1:114312400-114321200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr1:114312400-114321200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr1:114312600-114318800	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr1:114312600-114322600	Weak transcription	Brain Substantia Nigra	brain
38	chr1:114312600-114323600	Weak transcription	Right Atrium	heart
39	chr1:114312600-114323600	Weak transcription	Small Intestine	intestine
40	chr1:114312600-114328800	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr1:114312800-114319000	Weak transcription	Rectal Smooth Muscle	rectum
42	chr1:114312800-114321000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr1:114313200-114319000	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr1:114313200-114323600	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr1:114313400-114320400	Strong transcription	Dnd41	blood
46	chr1:114313400-114323600	Weak transcription	Brain Cingulate Gyrus	brain
47	chr1:114313400-114323800	Weak transcription	Brain Angular Gyrus	brain
48	chr1:114313600-114318800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr1:114314000-114323400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr1:114314200-114320000	Strong transcription	Primary T helper cells fromperipheralblood	blood

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