Variant report

Variant	rs12232351
Chromosome Location	chr15:56140995-56140996
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:56035905..56037422-chr15:56138325..56141165,2	MCF-7	breast:
2	chr15:56130240..56132919-chr15:56139346..56142252,2	K562	blood:

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1042477	0.82[ASN][1000 genomes]
rs10851599	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11071228	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11071231	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11630780	0.84[ASN][1000 genomes]
rs11632096	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11632977	0.84[ASN][1000 genomes]
rs11633263	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11633313	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12102014	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12102020	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12595359	0.80[AMR][1000 genomes]
rs12898589	0.83[ASN][1000 genomes]
rs12910830	0.82[ASN][1000 genomes]
rs13380185	0.81[ASN][1000 genomes]
rs1509406	0.96[CEU][hapmap];0.90[CHB][hapmap]
rs16976600	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1912398	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1912402	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2288344	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2288345	0.82[ASN][1000 genomes]
rs2414444	0.84[ASN][1000 genomes]
rs28660477	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35040841	0.82[ASN][1000 genomes]
rs56333939	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60482539	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs66462353	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs67505007	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7162435	1.00[CEU][hapmap];0.80[CHB][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7175686	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7176225	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7179116	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7182397	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72732282	0.82[EUR][1000 genomes]
rs8024944	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8026172	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8028559	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8029247	0.96[CEU][hapmap];0.86[CHB][hapmap]
rs8032158	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv457157	chr15:55722213-56255774	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv569539	chr15:55722213-56255774	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv833017	chr15:55965957-56157912	Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	esv3366380	chr15:56003224-56141650	Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12232351	PRTG	cis	Artery Tibial	GTEx

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56115400-56148000	Weak transcription	Ovary	ovary
2	chr15:56116600-56150600	Weak transcription	Right Ventricle	heart
3	chr15:56116800-56162200	Weak transcription	Fetal Heart	heart
4	chr15:56118600-56151000	Weak transcription	Fetal Kidney	kidney
5	chr15:56118800-56147000	Weak transcription	Gastric	stomach
6	chr15:56118800-56149200	Weak transcription	Brain Cingulate Gyrus	brain
7	chr15:56118800-56151400	Weak transcription	Brain Anterior Caudate	brain
8	chr15:56120000-56144800	Strong transcription	Skeletal Muscle Female	skeletal muscle
9	chr15:56120000-56147800	Weak transcription	HepG2	liver
10	chr15:56120600-56146600	Weak transcription	Pancreas	Pancrea
11	chr15:56120800-56147200	Weak transcription	Thymus	Thymus
12	chr15:56121200-56147200	Weak transcription	Spleen	Spleen
13	chr15:56122400-56145200	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr15:56122600-56152000	Weak transcription	Fetal Thymus	thymus
15	chr15:56122600-56153800	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr15:56122600-56154800	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr15:56122600-56156600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr15:56122800-56141600	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chr15:56122800-56147200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr15:56122800-56147600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr15:56122800-56156000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr15:56127200-56155400	Strong transcription	Osteobl	bone
23	chr15:56127200-56155800	Strong transcription	HSMM	muscle
24	chr15:56129000-56157400	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr15:56129600-56147400	Weak transcription	Esophagus	oesophagus
26	chr15:56129800-56146600	Weak transcription	NHLF	lung
27	chr15:56132000-56164800	Weak transcription	Small Intestine	intestine
28	chr15:56132800-56141000	Strong transcription	Muscle Satellite Cultured Cells	--
29	chr15:56133000-56142600	Weak transcription	Hela-S3	cervix
30	chr15:56133000-56152600	Weak transcription	Brain Hippocampus Middle	brain
31	chr15:56133600-56154400	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr15:56134200-56150600	Weak transcription	Left Ventricle	heart
33	chr15:56134400-56147400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr15:56134400-56150000	Weak transcription	Psoas Muscle	Psoas
35	chr15:56134400-56156600	Weak transcription	Colon Smooth Muscle	Colon
36	chr15:56134800-56151800	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr15:56135000-56156600	Weak transcription	Rectal Smooth Muscle	rectum
38	chr15:56135200-56146000	Weak transcription	Fetal Muscle Trunk	muscle
39	chr15:56135200-56152600	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr15:56135400-56147800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr15:56135600-56142800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr15:56135600-56145400	Weak transcription	HUVEC	blood vessel
43	chr15:56136200-56143800	Weak transcription	Primary T cells from cord blood	blood
44	chr15:56136400-56145800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr15:56138200-56161800	Weak transcription	K562	blood
46	chr15:56138400-56149000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr15:56138600-56144600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr15:56138600-56145000	Strong transcription	Fetal Intestine Large	intestine
49	chr15:56138600-56154400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr15:56138800-56152800	Weak transcription	GM12878-XiMat	blood

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