Variant report

Variant	rs12906680
Chromosome Location	chr15:56140180-56140181
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:56035905..56037422-chr15:56138325..56141165,2	MCF-7	breast:
2	chr15:56138547..56140362-chr15:56145607..56147733,2	MCF-7	breast:
3	chr15:56130240..56132919-chr15:56139346..56142252,2	K562	blood:

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10851598	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11071229	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1134352	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11635063	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11853453	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11858692	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12593446	0.82[EUR][1000 genomes]
rs12912488	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12912732	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16976653	1.00[CHB][hapmap];0.80[JPT][hapmap]
rs17819276	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17819294	0.82[EUR][1000 genomes]
rs1912404	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs28444575	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28448752	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3759865	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4774229	0.86[EUR][1000 genomes]
rs6493825	0.86[EUR][1000 genomes]
rs6493827	1.00[CHB][hapmap];0.80[JPT][hapmap]
rs7163864	1.00[CHB][hapmap];0.87[JPT][hapmap]
rs7180060	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7182280	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs9788664	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9888655	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9888676	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9920007	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[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

No data

Chromatin state (count:90 , 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	chr15:56123000-56140200	Weak transcription	Dnd41	blood
23	chr15:56127200-56155400	Strong transcription	Osteobl	bone
24	chr15:56127200-56155800	Strong transcription	HSMM	muscle
25	chr15:56129000-56157400	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr15:56129600-56147400	Weak transcription	Esophagus	oesophagus
27	chr15:56129800-56146600	Weak transcription	NHLF	lung
28	chr15:56130600-56140200	Strong transcription	A549	lung
29	chr15:56132000-56164800	Weak transcription	Small Intestine	intestine
30	chr15:56132800-56141000	Strong transcription	Muscle Satellite Cultured Cells	--
31	chr15:56133000-56142600	Weak transcription	Hela-S3	cervix
32	chr15:56133000-56152600	Weak transcription	Brain Hippocampus Middle	brain
33	chr15:56133600-56154400	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr15:56134200-56150600	Weak transcription	Left Ventricle	heart
35	chr15:56134400-56140200	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr15:56134400-56147400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr15:56134400-56150000	Weak transcription	Psoas Muscle	Psoas
38	chr15:56134400-56156600	Weak transcription	Colon Smooth Muscle	Colon
39	chr15:56134600-56140200	Weak transcription	Adipose Nuclei	Adipose
40	chr15:56134800-56140200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr15:56134800-56140200	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr15:56134800-56151800	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr15:56135000-56140200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr15:56135000-56156600	Weak transcription	Rectal Smooth Muscle	rectum
45	chr15:56135200-56140400	Weak transcription	Fetal Lung	lung
46	chr15:56135200-56146000	Weak transcription	Fetal Muscle Trunk	muscle
47	chr15:56135200-56152600	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr15:56135400-56140200	Weak transcription	Duodenum Mucosa	Duodenum
49	chr15:56135400-56147800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr15:56135600-56140200	Weak transcription	Stomach Smooth Muscle	stomach

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