Variant report

Variant	rs28576740
Chromosome Location	chr9:79273752-79273753
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:79073466..79074012-chr9:79273464..79274142,2	K562	blood:
2	chr9:79062041..79063533-chr9:79272880..79274341,6	MCF-7	breast:
3	chr9:79018295..79018910-chr9:79273206..79274160,3	MCF-7	breast:
4	chr9:79061368..79063776-chr9:79272393..79274903,3	MCF-7	breast:
5	chr9:79073452..79074417-chr9:79273251..79274110,4	MCF-7	breast:
6	chr9:79062067..79063554-chr9:79273134..79274136,17	MCF-7	breast:
7	chr9:79057879..79060217-chr9:79273582..79275232,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000187210	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10119518	1.00[EUR][1000 genomes]
rs10121652	1.00[EUR][1000 genomes]
rs10123325	1.00[EUR][1000 genomes]
rs10521473	1.00[EUR][1000 genomes]
rs11144991	1.00[EUR][1000 genomes]
rs11144993	1.00[EUR][1000 genomes]
rs12336287	1.00[EUR][1000 genomes]
rs12337785	1.00[EUR][1000 genomes]
rs12340696	1.00[EUR][1000 genomes]
rs12342460	1.00[EUR][1000 genomes]
rs12345816	1.00[EUR][1000 genomes]
rs12351220	1.00[EUR][1000 genomes]
rs1346041	1.00[EUR][1000 genomes]
rs17062959	1.00[EUR][1000 genomes]
rs17062964	1.00[EUR][1000 genomes]
rs17062967	1.00[EUR][1000 genomes]
rs17081141	1.00[EUR][1000 genomes]
rs17081142	1.00[EUR][1000 genomes]
rs2015354	1.00[EUR][1000 genomes]
rs28470485	1.00[EUR][1000 genomes]
rs28587388	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28635278	1.00[EUR][1000 genomes]
rs55725331	1.00[EUR][1000 genomes]
rs55825540	1.00[EUR][1000 genomes]
rs56026497	1.00[EUR][1000 genomes]
rs56143215	1.00[EUR][1000 genomes]
rs56145880	1.00[EUR][1000 genomes]
rs56679509	1.00[EUR][1000 genomes]
rs57802610	1.00[EUR][1000 genomes]
rs60467484	1.00[EUR][1000 genomes]
rs6560530	1.00[EUR][1000 genomes]
rs7044442	1.00[EUR][1000 genomes]
rs73449878	1.00[EUR][1000 genomes]
rs73449890	1.00[EUR][1000 genomes]
rs73449896	1.00[EUR][1000 genomes]
rs73452104	1.00[EUR][1000 genomes]
rs73454158	1.00[EUR][1000 genomes]
rs73650254	1.00[EUR][1000 genomes]
rs73650286	1.00[EUR][1000 genomes]
rs73650287	1.00[EUR][1000 genomes]
rs73650987	1.00[EUR][1000 genomes]
rs73650989	1.00[EUR][1000 genomes]
rs73650990	1.00[EUR][1000 genomes]
rs73650991	1.00[EUR][1000 genomes]
rs73650992	1.00[EUR][1000 genomes]
rs73650994	1.00[EUR][1000 genomes]
rs73650996	1.00[EUR][1000 genomes]
rs73650997	1.00[EUR][1000 genomes]
rs73650998	1.00[EUR][1000 genomes]
rs73650999	1.00[EUR][1000 genomes]
rs73651000	1.00[EUR][1000 genomes]
rs73651001	1.00[EUR][1000 genomes]
rs7848842	1.00[EUR][1000 genomes]
rs7850310	1.00[EUR][1000 genomes]
rs7855826	1.00[EUR][1000 genomes]
rs7867080	1.00[EUR][1000 genomes]
rs7875591	1.00[EUR][1000 genomes]
rs867646	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869152	chr9:78742197-79583399	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv931033	chr9:78850330-79366454	Genic enhancers Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv893479	chr9:78971253-79275226	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv949417	chr9:79078703-79282589	Strong transcription Genic enhancers Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv1040363	chr9:79246366-79711737	Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:79252600-79278000	Weak transcription	Gastric	stomach
2	chr9:79259000-79278000	Weak transcription	Spleen	Spleen
3	chr9:79260000-79282400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr9:79263600-79282200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr9:79265600-79274000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr9:79266000-79278000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr9:79266400-79306800	Weak transcription	Fetal Stomach	stomach
8	chr9:79266600-79274200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr9:79266600-79282200	Weak transcription	Brain Anterior Caudate	brain
10	chr9:79269000-79278000	Weak transcription	Aorta	Aorta
11	chr9:79269200-79275800	Weak transcription	Fetal Muscle Leg	muscle
12	chr9:79269400-79274000	Enhancers	Muscle Satellite Cultured Cells	--
13	chr9:79269400-79277000	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr9:79269800-79282200	Weak transcription	Brain Substantia Nigra	brain
15	chr9:79270400-79273800	Weak transcription	Brain Hippocampus Middle	brain
16	chr9:79270400-79277000	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr9:79270400-79277200	Weak transcription	GM12878-XiMat	blood
18	chr9:79270400-79303000	Weak transcription	Colon Smooth Muscle	Colon
19	chr9:79270600-79273800	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr9:79270600-79274000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr9:79270600-79274000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr9:79270600-79275000	Weak transcription	Brain Cingulate Gyrus	brain
23	chr9:79270600-79278800	Weak transcription	Brain Angular Gyrus	brain
24	chr9:79271400-79273800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr9:79271400-79274000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr9:79271600-79285200	Weak transcription	Rectal Smooth Muscle	rectum
27	chr9:79271800-79273800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr9:79271800-79274000	Enhancers	NHLF	lung
29	chr9:79272000-79273800	Enhancers	HSMMtube	muscle
30	chr9:79272000-79274000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr9:79272000-79274000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr9:79272000-79274000	Enhancers	HSMM	muscle
33	chr9:79272000-79276800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr9:79272200-79273800	Enhancers	Primary B cells from cord blood	blood
35	chr9:79272200-79277000	Weak transcription	Stomach Smooth Muscle	stomach
36	chr9:79272400-79274000	Enhancers	Stomach Mucosa	stomach
37	chr9:79272600-79277400	Weak transcription	Primary hematopoietic stem cells	blood
38	chr9:79272600-79282000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr9:79272800-79277000	Weak transcription	HUVEC	blood vessel
40	chr9:79273000-79274200	Enhancers	Primary hematopoietic stem cells short term culture	blood
41	chr9:79273200-79274000	Enhancers	Duodenum Mucosa	Duodenum
42	chr9:79273200-79274000	Enhancers	Fetal Intestine Small	intestine
43	chr9:79273200-79274200	Enhancers	Pancreatic Islets	Pancreatic Islet
44	chr9:79273400-79274000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr9:79273400-79274000	Enhancers	HUES6 Cell Line	embryonic stem cell
46	chr9:79273400-79274000	Enhancers	Primary monocytes fromperipheralblood	blood
47	chr9:79273400-79274000	Enhancers	Fetal Lung	lung
48	chr9:79273400-79274000	Enhancers	NHDF-Ad	bronchial
49	chr9:79273400-79274200	Enhancers	Fetal Thymus	thymus
50	chr9:79273400-79274400	Enhancers	Primary neutrophils fromperipheralblood	blood

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