Variant report

Variant	rs3099980
Chromosome Location	chr2:39054048-39054049
allele	A/G
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:39036853..39041014-chr2:39051745..39054794,3	K562	blood:
2	chr2:39053503..39057037-chr2:39058758..39062643,3	K562	blood:
3	chr2:39052271..39054519-chr2:39105359..39107014,2	K562	blood:
4	chr2:38976908..38981867-chr2:39050395..39056507,16	K562	blood:
5	chr2:38970642..38974334-chr2:39052366..39056279,4	K562	blood:
6	chr2:38974988..38979943-chr2:39053736..39058253,10	K562	blood:
7	chr2:39053934..39056407-chr2:39351577..39353846,2	K562	blood:
8	chr2:39053503..39055563-chr2:39060007..39062643,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000152147	Chromatin interaction
ENSG00000115875	Chromatin interaction
ENSG00000223922	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1979143	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3099961	0.89[ASN][1000 genomes]
rs3099965	0.90[ASN][1000 genomes]
rs3099968	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3099971	0.86[ASN][1000 genomes]
rs3099975	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3099977	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3099981	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3099990	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3099992	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3112142	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3112143	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3112150	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3112184	0.86[ASN][1000 genomes]
rs3112186	0.86[ASN][1000 genomes]
rs3112188	0.86[ASN][1000 genomes]
rs3112189	0.86[ASN][1000 genomes]
rs3112191	0.86[ASN][1000 genomes]
rs3112192	0.86[ASN][1000 genomes]
rs3112194	0.88[ASN][1000 genomes]
rs3112196	0.89[ASN][1000 genomes]
rs3112198	0.85[ASN][1000 genomes]
rs3112204	0.89[ASN][1000 genomes]
rs3134637	0.85[ASN][1000 genomes]
rs35387882	0.81[ASN][1000 genomes]
rs6544175	0.87[EUR][1000 genomes]
rs756338	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[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	nsv916059	chr2:38332341-39119398	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	143 gene(s)	inside rSNPs	diseases
2	nsv9646	chr2:38358311-39082189	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	141 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39006400-39085600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr2:39019000-39057800	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr2:39022000-39066800	Weak transcription	Stomach Mucosa	stomach
4	chr2:39026600-39079800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr2:39030600-39088200	Weak transcription	Fetal Heart	heart
6	chr2:39032800-39072800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr2:39037200-39055800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr2:39037400-39054600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr2:39038200-39056000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr2:39038800-39095600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr2:39038800-39102200	Weak transcription	Gastric	stomach
12	chr2:39039000-39085400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr2:39039000-39090000	Weak transcription	Esophagus	oesophagus
14	chr2:39039000-39101200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr2:39039000-39102000	Weak transcription	Colonic Mucosa	Colon
16	chr2:39040000-39069000	Strong transcription	Fetal Muscle Leg	muscle
17	chr2:39040600-39056000	Strong transcription	Cortex derived primary cultured neurospheres	brain
18	chr2:39040800-39054200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr2:39042800-39063000	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr2:39042800-39080600	Weak transcription	Small Intestine	intestine
21	chr2:39043600-39079800	Weak transcription	Right Ventricle	heart
22	chr2:39044800-39056800	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr2:39046000-39073200	Weak transcription	Pancreas	Pancrea
24	chr2:39046200-39070200	Weak transcription	NHLF	lung
25	chr2:39046400-39057200	Weak transcription	HepG2	liver
26	chr2:39048000-39055600	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr2:39048400-39054200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr2:39048400-39060800	Strong transcription	Fetal Stomach	stomach
29	chr2:39049000-39054400	Strong transcription	Placenta	Placenta
30	chr2:39049000-39056000	Strong transcription	Fetal Intestine Small	intestine
31	chr2:39049400-39054200	Strong transcription	Fetal Brain Female	brain
32	chr2:39049400-39054800	Strong transcription	HUES6 Cell Line	embryonic stem cell
33	chr2:39049400-39055400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
34	chr2:39049600-39054200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr2:39049600-39054200	Strong transcription	Primary B cells from peripheral blood	blood
36	chr2:39049600-39055600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr2:39049600-39055600	Strong transcription	Duodenum Smooth Muscle	Duodenum
38	chr2:39049600-39056200	Strong transcription	Fetal Intestine Large	intestine
39	chr2:39049800-39054200	Strong transcription	Fetal Muscle Trunk	muscle
40	chr2:39049800-39056000	Strong transcription	Brain Germinal Matrix	brain
41	chr2:39050000-39054200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr2:39050000-39055600	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr2:39050000-39055600	Strong transcription	Dnd41	blood
44	chr2:39050200-39054800	Strong transcription	K562	blood
45	chr2:39050400-39062800	Weak transcription	Thymus	Thymus
46	chr2:39050400-39063800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr2:39050400-39072800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr2:39050400-39079800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr2:39050400-39079800	Weak transcription	Spleen	Spleen
50	chr2:39050400-39088000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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