Variant report

Variant	rs55990139
Chromosome Location	chr9:96902441-96902442
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:96901466..96904094-chr9:96921471..96923356,3	K562	blood:
2	chr9:96899589..96905668-chr9:96926948..96930471,6	MCF-7	breast:
3	chr9:96855903..96857740-chr9:96900937..96903523,2	MCF-7	breast:
4	chr9:96901085..96902966-chr9:96921856..96923977,2	K562	blood:
5	chr9:96899950..96905236-chr9:96927673..96930558,7	K562	blood:
6	chr9:96899950..96904180-chr9:96926741..96930558,5	K562	blood:
7	chr9:96897901..96900583-chr9:96900946..96903604,5	MCF-7	breast:
8	chr9:96900996..96905420-chr9:96905582..96911723,7	K562	blood:
9	chr9:96901268..96903625-chr9:96924526..96926573,2	MCF-7	breast:
10	chr9:96897444..96899598-chr9:96901641..96904122,3	K562	blood:
11	chr9:96899016..96906502-chr9:96926750..96931118,14	MCF-7	breast:
12	chr9:96900977..96902501-chr9:96919516..96921302,2	K562	blood:
13	chr9:96901943..96905386-chr9:96905431..96909431,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000269946	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10761318	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10821299	1.00[AFR][1000 genomes]
rs10821302	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10821303	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10821304	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7854962	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7866254	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv482457	chr9:96813852-96996170	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	217 gene(s)	inside rSNPs	diseases
2	nsv831655	chr9:96834042-97042009	Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	218 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96897800-96902600	Weak transcription	Small Intestine	intestine
2	chr9:96899600-96903800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr9:96900400-96907400	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr9:96900800-96903200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr9:96901000-96904000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr9:96901200-96904600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr9:96901200-96904600	Enhancers	Fetal Muscle Leg	muscle
8	chr9:96901400-96903000	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr9:96901400-96903400	Enhancers	Rectal Smooth Muscle	rectum
10	chr9:96901400-96903600	Enhancers	Stomach Mucosa	stomach
11	chr9:96901400-96905800	Enhancers	Fetal Muscle Trunk	muscle
12	chr9:96901600-96902800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr9:96901600-96903400	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr9:96902000-96902800	Flanking Active TSS	A549	lung
15	chr9:96902000-96903200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
16	chr9:96902000-96903200	Flanking Active TSS	Hela-S3	cervix
17	chr9:96902000-96903400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr9:96902000-96904200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr9:96902000-96904600	Enhancers	Fetal Stomach	stomach
20	chr9:96902200-96902600	Flanking Active TSS	HUVEC	blood vessel
21	chr9:96902200-96902800	Flanking Active TSS	Adipose Nuclei	Adipose
22	chr9:96902200-96902800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
23	chr9:96902200-96902800	Flanking Active TSS	K562	blood
24	chr9:96902200-96902800	Flanking Active TSS	Osteobl	bone
25	chr9:96902200-96903000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr9:96902200-96903000	Enhancers	Fetal Kidney	kidney
27	chr9:96902200-96903000	Enhancers	Rectal Mucosa Donor 31	rectum
28	chr9:96902200-96903000	Enhancers	HepG2	liver
29	chr9:96902200-96903200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr9:96902200-96903600	Enhancers	Brain Cingulate Gyrus	brain
31	chr9:96902200-96903800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr9:96902200-96903800	Enhancers	Brain Angular Gyrus	brain
33	chr9:96902200-96904200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr9:96902200-96904400	Enhancers	Colon Smooth Muscle	Colon
35	chr9:96902200-96904600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr9:96902200-96904600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr9:96902200-96904600	Enhancers	Lung	lung
38	chr9:96902200-96904800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr9:96902200-96905400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr9:96902400-96902600	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
41	chr9:96902400-96902600	Active TSS	Duodenum Smooth Muscle	Duodenum
42	chr9:96902400-96902600	Flanking Active TSS	HMEC	breast
43	chr9:96902400-96902800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr9:96902400-96902800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr9:96902400-96902800	Flanking Active TSS	Brain Hippocampus Middle	brain
46	chr9:96902400-96902800	Flanking Active TSS	Fetal Lung	lung
47	chr9:96902400-96902800	Enhancers	Pancreas	Pancrea
48	chr9:96902400-96902800	Enhancers	Placenta Amnion	Placenta Amnion
49	chr9:96902400-96902800	Enhancers	Rectal Mucosa Donor 29	rectum
50	chr9:96902400-96902800	Enhancers	Sigmoid Colon	Sigmoid Colon

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