Variant report

Variant	rs12005884
Chromosome Location	chr9:86049412-86049413
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:86046794..86050465-chr9:86050692..86054566,4	MCF-7	breast:

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10217271	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10217435	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10217669	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10217746	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10217752	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11140068	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11140071	1.00[CEU][hapmap];0.80[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11140080	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11140081	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11140085	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11998876	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12000173	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12337733	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12339003	0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12340422	0.88[CEU][hapmap];0.84[CHB][hapmap]
rs12346296	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12350642	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12551179	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12553050	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17086251	0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs3893399	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61424289	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73465724	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73465767	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[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	nsv1046491	chr9:85861492-86063992	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv893512	chr9:86022215-86323309	Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Strong transcription Bivalent/Poised TSS 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 miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1048086	chr9:86040900-86059732	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:86039200-86050000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr9:86040400-86050000	Weak transcription	Fetal Intestine Large	intestine
3	chr9:86046600-86050800	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr9:86047200-86052200	Enhancers	Rectal Mucosa Donor 31	rectum
5	chr9:86047400-86050400	Enhancers	HepG2	liver
6	chr9:86047400-86052600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr9:86047400-86056600	Weak transcription	Stomach Smooth Muscle	stomach
8	chr9:86047400-86059000	Weak transcription	Placenta	Placenta
9	chr9:86047600-86051200	Weak transcription	Fetal Heart	heart
10	chr9:86047600-86052400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr9:86047600-86053800	Weak transcription	Aorta	Aorta
12	chr9:86047600-86055800	Weak transcription	Esophagus	oesophagus
13	chr9:86047600-86055800	Weak transcription	Ovary	ovary
14	chr9:86047600-86059200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr9:86047600-86062400	Weak transcription	Colon Smooth Muscle	Colon
16	chr9:86048000-86050600	Enhancers	Primary neutrophils fromperipheralblood	blood
17	chr9:86048200-86056400	Weak transcription	A549	lung
18	chr9:86048600-86049600	Enhancers	Adipose Nuclei	Adipose
19	chr9:86048600-86049600	Enhancers	Rectal Mucosa Donor 29	rectum
20	chr9:86048600-86049600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
21	chr9:86048600-86049800	Enhancers	Skeletal Muscle Male	skeletal muscle
22	chr9:86048600-86051200	Enhancers	Left Ventricle	heart
23	chr9:86048800-86052000	Enhancers	Sigmoid Colon	Sigmoid Colon
24	chr9:86049200-86050000	Enhancers	Right Ventricle	heart
25	chr9:86049400-86050200	Weak transcription	Pancreas	Pancrea
26	chr9:86049400-86050400	Weak transcription	Psoas Muscle	Psoas
27	chr9:86049400-86050800	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr9:86049400-86055200	Weak transcription	Gastric	stomach
29	chr9:86049400-86055200	Weak transcription	Spleen	Spleen
30	chr9:86049400-86055600	Weak transcription	Right Atrium	heart

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