Variant report

Variant	rs3789599
Chromosome Location	chr1:114323318-114323319
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:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:114317877..114322132-chr1:114322334..114326038,5	K562	blood:
2	chr1:114299550..114305587-chr1:114319005..114326238,14	MCF-7	breast:
3	chr1:114323280..114325938-chr1:114345908..114348853,2	MCF-7	breast:
4	chr1:114318613..114321495-chr1:114322094..114326471,4	MCF-7	breast:
5	chr1:114323200..114325575-chr1:114326515..114328843,2	K562	blood:
6	chr1:114306321..114309666-chr1:114320430..114324834,4	MCF-7	breast:
7	chr1:114322818..114325422-chr1:114354034..114355879,2	K562	blood:
8	chr1:114310669..114312600-chr1:114322357..114324500,2	MCF-7	breast:
9	chr1:114312977..114314821-chr1:114322863..114325165,2	MCF-7	breast:
10	chr1:114319916..114324348-chr1:114352718..114356964,7	MCF-7	breast:
11	chr1:114320491..114326144-chr1:114352849..114356180,5	MCF-7	breast:
12	chr1:114301214..114302761-chr1:114321511..114324430,2	MCF-7	breast:
13	chr1:114317996..114324872-chr1:114329159..114335059,8	K562	blood:
14	chr1:114322719..114325037-chr1:114328729..114331001,2	MCF-7	breast:
15	chr1:114323264..114325037-chr1:114328187..114331167,2	MCF-7	breast:

No data

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

Extended variants
information (count: 37 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10127930	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10489936	0.83[CEU][hapmap];1.00[CHB][hapmap]
rs1080307	0.83[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap]
rs1217384	0.94[CHD][hapmap];0.93[GIH][hapmap];0.90[MEX][hapmap]
rs12730735	0.81[ASN][1000 genomes]
rs12734625	0.81[ASN][1000 genomes]
rs12735104	0.86[ASN][1000 genomes]
rs12748727	0.81[ASN][1000 genomes]
rs12752932	0.81[ASN][1000 genomes]
rs12760457	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.81[ASN][1000 genomes]
rs13374352	0.81[ASN][1000 genomes]
rs17274634	0.83[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap]
rs17462614	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17509390	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1885454	0.83[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap]
rs2040040	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2359173	0.83[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap]
rs2359174	0.83[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap]
rs34042871	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs34341173	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs34649199	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs36115604	0.81[ASN][1000 genomes]
rs3747998	0.83[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap]
rs3748003	0.83[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap]
rs3761931	0.83[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap]
rs3789607	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.86[ASN][1000 genomes]
rs3789609	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap]
rs61817586	0.81[ASN][1000 genomes]
rs61817617	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6668829	0.83[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6674848	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap];0.81[ASN][1000 genomes]
rs6703387	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7533605	0.81[ASN][1000 genomes]
rs7555354	0.81[ASN][1000 genomes]
rs9803891	0.83[CEU][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3789599	CD58	cis	cerebellum	SCAN
rs3789599	MAGI3	cis	parietal	SCAN
rs3789599	PHTF1	cis	cerebellum	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:114302800-114323600	Weak transcription	Psoas Muscle	Psoas
2	chr1:114302800-114326000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr1:114302800-114326200	Weak transcription	Pancreas	Pancrea
4	chr1:114302800-114326200	Weak transcription	Right Ventricle	heart
5	chr1:114303000-114326200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr1:114303200-114328400	Weak transcription	A549	lung
7	chr1:114303400-114353800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:114308200-114326600	Weak transcription	Colonic Mucosa	Colon
9	chr1:114309000-114323600	Weak transcription	Gastric	stomach
10	chr1:114309600-114353400	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr1:114310600-114325400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr1:114310800-114326000	Weak transcription	HMEC	breast
13	chr1:114311000-114323600	Weak transcription	Lung	lung
14	chr1:114311000-114324800	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr1:114311000-114325800	Weak transcription	Stomach Smooth Muscle	stomach
16	chr1:114311000-114326200	Weak transcription	HUVEC	blood vessel
17	chr1:114311000-114335600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr1:114311000-114336800	Weak transcription	Fetal Kidney	kidney
19	chr1:114311000-114341800	Weak transcription	Esophagus	oesophagus
20	chr1:114311200-114325800	Weak transcription	NHEK	skin
21	chr1:114312600-114323600	Weak transcription	Right Atrium	heart
22	chr1:114312600-114323600	Weak transcription	Small Intestine	intestine
23	chr1:114312600-114328800	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr1:114313200-114323600	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr1:114313400-114323600	Weak transcription	Brain Cingulate Gyrus	brain
26	chr1:114313400-114323800	Weak transcription	Brain Angular Gyrus	brain
27	chr1:114314000-114323400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr1:114314200-114323600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr1:114317800-114326200	Weak transcription	Ovary	ovary
30	chr1:114318000-114326200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr1:114319400-114323400	Weak transcription	Brain Hippocampus Middle	brain
32	chr1:114319400-114323400	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr1:114319400-114323600	Weak transcription	HSMM	muscle
34	chr1:114319400-114324400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr1:114319400-114324600	Weak transcription	Adipose Nuclei	Adipose
36	chr1:114319400-114324600	Weak transcription	Brain Anterior Caudate	brain
37	chr1:114319400-114324800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr1:114319400-114325000	Weak transcription	Rectal Smooth Muscle	rectum
39	chr1:114319400-114325200	Weak transcription	Fetal Brain Female	brain
40	chr1:114319600-114323400	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr1:114319600-114325000	Weak transcription	NHDF-Ad	bronchial
42	chr1:114319800-114323400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr1:114319800-114325800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr1:114319800-114326400	Weak transcription	Hela-S3	cervix
45	chr1:114319800-114352600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr1:114320000-114323400	Weak transcription	Osteobl	bone
47	chr1:114320000-114323600	Weak transcription	Liver	Liver
48	chr1:114320000-114323600	Weak transcription	Fetal Muscle Leg	muscle
49	chr1:114320000-114323600	Weak transcription	Left Ventricle	heart
50	chr1:114320000-114323600	Weak transcription	Spleen	Spleen

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