Variant report

Variant	rs3893398
Chromosome Location	chr9:86045872-86045873
allele	C/G
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]
rs10115207	0.88[MEX][hapmap]
rs10780604	0.84[CEU][hapmap]
rs10868004	0.95[CHB][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs10868007	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11140087	0.81[JPT][hapmap]
rs11140088	1.00[ASW][hapmap];0.95[LWK][hapmap];0.92[MEX][hapmap];0.96[MKK][hapmap];0.87[YRI][hapmap];0.93[AFR][1000 genomes]
rs2375919	0.88[MEX][hapmap]
rs3849868	0.87[YRI][hapmap];0.93[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs3860917	0.88[MEX][hapmap]
rs3860921	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3860924	0.88[MEX][hapmap]
rs4097498	0.88[MEX][hapmap]
rs4877761	0.82[CEU][hapmap];0.88[MEX][hapmap];0.81[AMR][1000 genomes]
rs4877762	0.88[MEX][hapmap]
rs4877763	0.86[YRI][hapmap];0.93[AFR][1000 genomes]
rs7019130	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7023415	0.86[YRI][hapmap];0.93[AFR][1000 genomes]
rs7035287	0.87[MEX][hapmap]
rs7037329	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7037659	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[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:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:86037800-86047200	Weak transcription	Fetal Stomach	stomach
2	chr9:86038400-86046600	Weak transcription	Rectal Smooth Muscle	rectum
3	chr9:86039200-86050000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr9:86040000-86046000	Weak transcription	Fetal Heart	heart
5	chr9:86040200-86046600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr9:86040400-86050000	Weak transcription	Fetal Intestine Large	intestine
7	chr9:86041800-86046000	Weak transcription	Duodenum Mucosa	Duodenum
8	chr9:86041800-86046600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr9:86041800-86046600	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr9:86041800-86047000	Weak transcription	Brain Angular Gyrus	brain
11	chr9:86042200-86046600	Weak transcription	Primary monocytes fromperipheralblood	blood
12	chr9:86042200-86046800	Weak transcription	Lung	lung
13	chr9:86042400-86046000	Weak transcription	Right Ventricle	heart
14	chr9:86042400-86046600	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr9:86043800-86046000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr9:86044000-86047600	Enhancers	Pancreas	Pancrea
17	chr9:86044400-86047600	Enhancers	Left Ventricle	heart
18	chr9:86044800-86046800	Enhancers	HepG2	liver
19	chr9:86045000-86046200	Enhancers	Fetal Muscle Trunk	muscle
20	chr9:86045000-86047600	Enhancers	Fetal Muscle Leg	muscle
21	chr9:86045200-86046800	Enhancers	Skeletal Muscle Female	skeletal muscle
22	chr9:86045400-86046600	Enhancers	A549	lung
23	chr9:86045600-86046200	Enhancers	Gastric	stomach
24	chr9:86045600-86046400	Enhancers	Fetal Brain Male	brain
25	chr9:86045600-86046600	Enhancers	Stomach Smooth Muscle	stomach
26	chr9:86045600-86047000	Enhancers	Adipose Nuclei	Adipose
27	chr9:86045600-86047400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr9:86045600-86047600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr9:86045600-86047600	Enhancers	Aorta	Aorta
30	chr9:86045600-86047600	Enhancers	Colon Smooth Muscle	Colon
31	chr9:86045600-86047600	Enhancers	Ovary	ovary
32	chr9:86045600-86047600	Enhancers	Right Atrium	heart
33	chr9:86045600-86048200	Enhancers	Liver	Liver
34	chr9:86045800-86046000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
35	chr9:86045800-86046000	Enhancers	Brain Cingulate Gyrus	brain
36	chr9:86045800-86046000	Enhancers	Small Intestine	intestine
37	chr9:86045800-86046200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr9:86045800-86046200	Enhancers	Brain Hippocampus Middle	brain
39	chr9:86045800-86046600	Enhancers	Rectal Mucosa Donor 31	rectum
40	chr9:86045800-86046600	Enhancers	Hela-S3	cervix
41	chr9:86045800-86046800	Enhancers	Duodenum Smooth Muscle	Duodenum
42	chr9:86045800-86047400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr9:86045800-86047400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr9:86045800-86047400	Enhancers	Muscle Satellite Cultured Cells	--
45	chr9:86045800-86047400	Enhancers	Fetal Lung	lung
46	chr9:86045800-86047400	Enhancers	HSMMtube	muscle
47	chr9:86045800-86047600	Enhancers	Breast Myoepithelial Primary Cells	Breast
48	chr9:86045800-86047600	Enhancers	Psoas Muscle	Psoas
49	chr9:86045800-86047600	Enhancers	Spleen	Spleen
50	chr9:86045800-86048000	Enhancers	NHDF-Ad	bronchial

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