Variant report

Variant	rs3860920
Chromosome Location	chr9:86045773-86045774
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	chr9:86045543..86047511-chr9:86062619..86064900,2	MCF-7	breast:

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs17086243	1.00[CHB][hapmap];0.84[JPT][hapmap];0.95[ASN][1000 genomes]
rs17086262	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs17086263	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs3860922	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3860923	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs55723059	0.86[AFR][1000 genomes]
rs60581387	0.97[ASN][1000 genomes]
rs72745063	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72745065	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72745066	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72745068	0.86[AFR][1000 genomes]
rs72745070	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72745075	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72745077	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72745079	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72745085	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72745088	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72745094	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72745098	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72745100	0.86[AFR][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:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:86037800-86047200	Weak transcription	Fetal Stomach	stomach
2	chr9:86038400-86045800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr9:86038400-86046600	Weak transcription	Rectal Smooth Muscle	rectum
4	chr9:86039200-86050000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr9:86040000-86045800	Weak transcription	Fetal Lung	lung
6	chr9:86040000-86045800	Weak transcription	Small Intestine	intestine
7	chr9:86040000-86046000	Weak transcription	Fetal Heart	heart
8	chr9:86040200-86046600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr9:86040400-86045800	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr9:86040400-86050000	Weak transcription	Fetal Intestine Large	intestine
11	chr9:86041600-86045800	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr9:86041800-86045800	Weak transcription	Spleen	Spleen
13	chr9:86041800-86046000	Weak transcription	Duodenum Mucosa	Duodenum
14	chr9:86041800-86046600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr9:86041800-86046600	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr9:86041800-86047000	Weak transcription	Brain Angular Gyrus	brain
17	chr9:86042200-86045800	Weak transcription	Brain Cingulate Gyrus	brain
18	chr9:86042200-86045800	Weak transcription	Psoas Muscle	Psoas
19	chr9:86042200-86045800	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr9:86042200-86046600	Weak transcription	Primary monocytes fromperipheralblood	blood
21	chr9:86042200-86046800	Weak transcription	Lung	lung
22	chr9:86042400-86045800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr9:86042400-86046000	Weak transcription	Right Ventricle	heart
24	chr9:86042400-86046600	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr9:86043800-86046000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr9:86044000-86047600	Enhancers	Pancreas	Pancrea
27	chr9:86044400-86047600	Enhancers	Left Ventricle	heart
28	chr9:86044800-86046800	Enhancers	HepG2	liver
29	chr9:86045000-86046200	Enhancers	Fetal Muscle Trunk	muscle
30	chr9:86045000-86047600	Enhancers	Fetal Muscle Leg	muscle
31	chr9:86045200-86046800	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr9:86045400-86046600	Enhancers	A549	lung
33	chr9:86045600-86046200	Enhancers	Gastric	stomach
34	chr9:86045600-86046400	Enhancers	Fetal Brain Male	brain
35	chr9:86045600-86046600	Enhancers	Stomach Smooth Muscle	stomach
36	chr9:86045600-86047000	Enhancers	Adipose Nuclei	Adipose
37	chr9:86045600-86047400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr9:86045600-86047600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr9:86045600-86047600	Enhancers	Aorta	Aorta
40	chr9:86045600-86047600	Enhancers	Colon Smooth Muscle	Colon
41	chr9:86045600-86047600	Enhancers	Ovary	ovary
42	chr9:86045600-86047600	Enhancers	Right Atrium	heart
43	chr9:86045600-86048200	Enhancers	Liver	Liver

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