Variant report

Variant	rs28488898
Chromosome Location	chr9:116098510-116098511
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:116091769..116094261-chr9:116096086..116099687,3	MCF-7	breast:
2	chr9:116097146..116099824-chr9:116100813..116103187,4	MCF-7	breast:
3	chr9:116097716..116100353-chr9:116171832..116173632,2	MCF-7	breast:
4	chr9:116098488..116100894-chr9:116162238..116164965,2	MCF-7	breast:
5	chr9:116071207..116072159-chr9:116097719..116098604,2	K562	blood:
6	chr9:116035986..116039204-chr9:116098421..116104240,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000148229	Chromatin interaction
ENSG00000136875	Chromatin interaction
ENSG00000157653	Chromatin interaction
ENSG00000176386	Chromatin interaction
ENSG00000148225	Chromatin interaction
ENSG00000148218	Chromatin interaction

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

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

rs_ID	r²[population]
rs10114352	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10118304	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10120336	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10122035	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10481672	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10481673	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10481675	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10981753	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12336439	0.85[AMR][1000 genomes]
rs12337069	0.85[AMR][1000 genomes]
rs12337123	0.85[AMR][1000 genomes]
rs12339006	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12345499	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12346510	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12347798	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12348236	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12348581	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12350255	0.85[AMR][1000 genomes]
rs12350332	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12350377	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12352852	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12352895	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28375224	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28393902	1.00[AMR][1000 genomes]
rs28536744	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28556819	0.85[AMR][1000 genomes]
rs28597401	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28725394	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7850003	0.84[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	nsv530949	chr9:115821128-116487796	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv1042663	chr9:115920158-116167140	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv893744	chr9:115934852-116170227	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116073800-116101600	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr9:116077400-116101400	Weak transcription	Brain Germinal Matrix	brain
3	chr9:116077400-116101600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr9:116077800-116101200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr9:116080800-116101400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr9:116080800-116101600	Weak transcription	Fetal Brain Male	brain
7	chr9:116081000-116101600	Weak transcription	Pancreas	Pancrea
8	chr9:116082200-116101600	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr9:116082600-116101400	Weak transcription	Primary hematopoietic stem cells	blood
10	chr9:116082800-116101400	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr9:116082800-116101600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr9:116082800-116101600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr9:116082800-116101600	Weak transcription	Brain Substantia Nigra	brain
14	chr9:116082800-116101600	Weak transcription	Fetal Kidney	kidney
15	chr9:116082800-116101600	Weak transcription	Fetal Muscle Trunk	muscle
16	chr9:116082800-116102000	Weak transcription	Aorta	Aorta
17	chr9:116083000-116101400	Weak transcription	Brain Cingulate Gyrus	brain
18	chr9:116083800-116101200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr9:116083800-116101200	Weak transcription	Colon Smooth Muscle	Colon
20	chr9:116083800-116101400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr9:116083800-116101600	Weak transcription	Right Ventricle	heart
22	chr9:116084000-116101400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr9:116084200-116101200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr9:116084200-116101400	Weak transcription	Liver	Liver
25	chr9:116084200-116101400	Weak transcription	Brain Anterior Caudate	brain
26	chr9:116084200-116101400	Weak transcription	Fetal Stomach	stomach
27	chr9:116084200-116101600	Weak transcription	Fetal Muscle Leg	muscle
28	chr9:116085400-116101400	Weak transcription	Adipose Nuclei	Adipose
29	chr9:116085400-116101400	Weak transcription	Fetal Lung	lung
30	chr9:116085400-116101600	Weak transcription	Brain Angular Gyrus	brain
31	chr9:116085600-116101200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr9:116091400-116101400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr9:116092000-116101400	Weak transcription	Small Intestine	intestine
34	chr9:116093000-116101400	Weak transcription	Fetal Intestine Small	intestine
35	chr9:116093000-116101800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr9:116093600-116101200	Weak transcription	Stomach Smooth Muscle	stomach
37	chr9:116094400-116101200	Weak transcription	Left Ventricle	heart
38	chr9:116094400-116101400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr9:116094400-116101600	Weak transcription	Ovary	ovary
40	chr9:116095000-116101600	Weak transcription	Duodenum Mucosa	Duodenum
41	chr9:116097800-116099400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr9:116098400-116101400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr9:116098400-116101400	Weak transcription	NHDF-Ad	bronchial

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