Variant report

Variant	rs1552889
Chromosome Location	chr6:151019278-151019279
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:150856840..150859421-chr6:151018731..151021434,2	MCF-7	breast:

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs12661140	0.81[AMR][1000 genomes]
rs12663498	0.80[AMR][1000 genomes]
rs1494308	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1552886	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1552888	0.89[AFR][1000 genomes]
rs17080087	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs17080089	0.82[AMR][1000 genomes]
rs17080091	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs17080093	0.82[AMR][1000 genomes]
rs17080102	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs57139556	0.82[AMR][1000 genomes]
rs62434120	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs62434122	0.82[AMR][1000 genomes]
rs62434123	0.82[AMR][1000 genomes]
rs62434124	0.82[AMR][1000 genomes]
rs62434125	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs62434129	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs654698	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6557082	0.80[AMR][1000 genomes]
rs6557083	0.80[AMR][1000 genomes]
rs6919871	0.80[AMR][1000 genomes]
rs6921304	0.89[AFR][1000 genomes]
rs6929935	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9322273	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9322274	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9322275	0.95[AMR][1000 genomes]
rs9322277	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9322278	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9397343	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv886772	chr6:150743364-151024280	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1030326	chr6:150967665-151641372	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer 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	25 gene(s)	inside rSNPs	diseases
3	nsv966635	chr6:151018787-151025050	Weak transcription Enhancers Genic enhancers Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:151009000-151021200	Weak transcription	Fetal Muscle Trunk	muscle
2	chr6:151012200-151023800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr6:151013000-151020600	Enhancers	Primary B cells from cord blood	blood
4	chr6:151014600-151021000	Enhancers	Primary B cells from peripheral blood	blood
5	chr6:151015000-151020600	Weak transcription	Left Ventricle	heart
6	chr6:151015200-151033200	Weak transcription	Right Atrium	heart
7	chr6:151015400-151025600	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr6:151016800-151019400	Enhancers	Brain Substantia Nigra	brain
9	chr6:151017400-151020600	Weak transcription	Brain Hippocampus Middle	brain
10	chr6:151017600-151023800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr6:151017600-151029200	Weak transcription	Lung	lung
12	chr6:151017800-151025200	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr6:151017800-151025600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr6:151017800-151027200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr6:151018200-151019600	Enhancers	Liver	Liver
16	chr6:151018600-151021200	Weak transcription	Brain Cingulate Gyrus	brain
17	chr6:151018800-151020600	Weak transcription	Fetal Muscle Leg	muscle
18	chr6:151018800-151023800	Weak transcription	Fetal Thymus	thymus
19	chr6:151018800-151024000	Weak transcription	Placenta	Placenta
20	chr6:151018800-151028600	Weak transcription	Adipose Nuclei	Adipose
21	chr6:151019000-151020400	Weak transcription	Spleen	Spleen
22	chr6:151019000-151021200	Weak transcription	Fetal Stomach	stomach
23	chr6:151019000-151021400	Weak transcription	Thymus	Thymus
24	chr6:151019000-151033000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr6:151019000-151033200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr6:151019000-151035200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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