Variant report

Variant	rs28468571
Chromosome Location	chr9:98262735-98262736
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:98077549..98081770-chr9:98260761..98263260,3	MCF-7	breast:
2	chr9:98261417..98264468-chr9:98264904..98267634,4	MCF-7	breast:
3	chr9:98255984..98258555-chr9:98260350..98263528,4	K562	blood:
4	chr9:98262143..98268122-chr9:98269863..98275996,9	MCF-7	breast:
5	chr9:98253775..98259048-chr9:98260307..98264013,8	K562	blood:
6	chr9:98262094..98265423-chr9:98266222..98270404,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000271155	Chromatin interaction
ENSG00000158169	Chromatin interaction
ENSG00000271314	Chromatin interaction
ENSG00000185920	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs17368876	0.81[EUR][1000 genomes]
rs17369383	0.83[EUR][1000 genomes]
rs1877456	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2274693	0.82[EUR][1000 genomes]
rs2274694	0.82[EUR][1000 genomes]
rs2297087	0.82[EUR][1000 genomes]
rs28394554	0.82[EUR][1000 genomes]
rs28410513	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28411363	0.83[EUR][1000 genomes]
rs28412122	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28442014	0.82[EUR][1000 genomes]
rs28485705	0.95[EUR][1000 genomes]
rs28488553	0.83[EUR][1000 genomes]
rs28491365	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28504341	0.83[EUR][1000 genomes]
rs28633576	0.81[EUR][1000 genomes]
rs28702657	0.82[EUR][1000 genomes]
rs28704635	0.85[EUR][1000 genomes]
rs28705285	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3758301	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62558340	0.82[EUR][1000 genomes]
rs9632897	0.81[EUR][1000 genomes]
rs9632898	0.81[EUR][1000 genomes]
rs9632916	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531633	chr9:98078300-98431120	Flanking Active TSS Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	nsv831658	chr9:98152971-98342178	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv430083	chr9:98204245-98445645	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv1051665	chr9:98234404-98264577	Weak transcription Bivalent Enhancer Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv824994	chr9:98239963-98314431	Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv824995	chr9:98243455-98326547	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv824996	chr9:98245375-98283861	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' 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:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98223400-98266400	Weak transcription	Hela-S3	cervix
2	chr9:98240200-98267400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr9:98242400-98266400	Weak transcription	HSMMtube	muscle
4	chr9:98242800-98266600	Weak transcription	Adipose Nuclei	Adipose
5	chr9:98243000-98267800	Weak transcription	Aorta	Aorta
6	chr9:98249200-98263600	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr9:98250400-98262800	Weak transcription	Stomach Mucosa	stomach
8	chr9:98254000-98267400	Weak transcription	Small Intestine	intestine
9	chr9:98255600-98265000	Genic enhancers	Fetal Stomach	stomach
10	chr9:98257000-98262800	Enhancers	Brain Substantia Nigra	brain
11	chr9:98257000-98264200	Weak transcription	Fetal Muscle Trunk	muscle
12	chr9:98257000-98264200	Weak transcription	Gastric	stomach
13	chr9:98257400-98264400	Genic enhancers	Fetal Lung	lung
14	chr9:98257400-98266600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr9:98257400-98267000	Enhancers	Brain Hippocampus Middle	brain
16	chr9:98258000-98264200	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr9:98258000-98266400	Enhancers	Ovary	ovary
18	chr9:98258600-98266400	Weak transcription	Esophagus	oesophagus
19	chr9:98259600-98263000	Enhancers	Placenta	Placenta
20	chr9:98259600-98263000	Enhancers	Lung	lung
21	chr9:98259600-98263000	Enhancers	NHLF	lung
22	chr9:98259600-98266600	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr9:98259800-98263000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr9:98259800-98263000	Enhancers	Brain Anterior Caudate	brain
25	chr9:98260000-98262800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr9:98260000-98264200	Weak transcription	Psoas Muscle	Psoas
27	chr9:98260000-98266400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr9:98260000-98266600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr9:98260200-98264400	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr9:98260200-98264600	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr9:98260200-98264800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr9:98260400-98263400	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr9:98260400-98264200	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr9:98260400-98265200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr9:98260400-98265400	Weak transcription	A549	lung
36	chr9:98260400-98266400	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr9:98260400-98266400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr9:98260400-98266400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr9:98260600-98263400	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr9:98260600-98264000	Weak transcription	Fetal Brain Female	brain
41	chr9:98260800-98266400	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr9:98260800-98266400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr9:98260800-98266400	Weak transcription	NHDF-Ad	bronchial
44	chr9:98260800-98266600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr9:98260800-98267000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr9:98261200-98262800	Enhancers	HMEC	breast
47	chr9:98261200-98263200	Strong transcription	Fetal Intestine Large	intestine
48	chr9:98261200-98263400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr9:98261200-98265400	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr9:98261400-98263000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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