Variant report

Variant	rs9829002
Chromosome Location	chr3:51468858-51468859
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:51468826-51468946	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
VPRBP	TF binding region
ENSG00000270692	TF binding region

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

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs13316894	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13317936	1.00[AMR][1000 genomes]
rs13321111	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13322621	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13327225	1.00[AMR][1000 genomes]
rs13353505	1.00[AMR][1000 genomes]
rs28454463	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28626048	1.00[AMR][1000 genomes]
rs28890042	1.00[AMR][1000 genomes]
rs6777506	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6779163	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6806124	1.00[AMR][1000 genomes]
rs7635546	1.00[AMR][1000 genomes]
rs9812682	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9826415	1.00[AMR][1000 genomes]
rs9828325	1.00[AMR][1000 genomes]
rs9841963	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9846343	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9853900	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9855214	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9868612	1.00[AMR][1000 genomes]
rs9875513	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9878053	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014464	chr3:51220151-51909780	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv460536	chr3:51395571-51469107	Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv590276	chr3:51395571-51469107	Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv590277	chr3:51408051-51474418	Strong transcription Active TSS Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	esv3369762	chr3:51449727-51469314	Strong transcription Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	esv3444499	chr3:51449727-51469614	Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 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	chr3:51431400-51471200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr3:51433400-51477400	Weak transcription	Fetal Heart	heart
3	chr3:51434000-51475600	Strong transcription	Primary T cells fromperipheralblood	blood
4	chr3:51434200-51477600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr3:51434600-51471000	Weak transcription	Stomach Mucosa	stomach
6	chr3:51435200-51478000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:51439800-51478000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr3:51440800-51478200	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr3:51444800-51477800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr3:51445400-51478400	Strong transcription	Primary B cells from peripheral blood	blood
11	chr3:51446200-51471000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr3:51451200-51476800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr3:51451400-51469600	Strong transcription	Fetal Stomach	stomach
14	chr3:51458000-51474800	Weak transcription	K562	blood
15	chr3:51458200-51474400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr3:51458200-51474600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr3:51458200-51475200	Weak transcription	NHLF	lung
18	chr3:51458200-51475400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr3:51458200-51477600	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr3:51458200-51478400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr3:51458200-51489400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr3:51458200-51515000	Weak transcription	Fetal Brain Male	brain
23	chr3:51458400-51473000	Weak transcription	Pancreas	Pancrea
24	chr3:51458400-51474200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr3:51458400-51475400	Weak transcription	Gastric	stomach
26	chr3:51458400-51500200	Weak transcription	Psoas Muscle	Psoas
27	chr3:51458800-51503800	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr3:51460000-51472400	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr3:51460000-51475400	Weak transcription	Aorta	Aorta
30	chr3:51460200-51474000	Weak transcription	A549	lung
31	chr3:51461800-51478000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr3:51462400-51478200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr3:51462600-51469000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr3:51462600-51470600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr3:51462600-51476000	Strong transcription	Primary T cells from cord blood	blood
36	chr3:51462600-51477000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr3:51462600-51477200	Strong transcription	Placenta	Placenta
38	chr3:51462600-51477400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
39	chr3:51462600-51477400	Strong transcription	Rectal Mucosa Donor 29	rectum
40	chr3:51462800-51475400	Strong transcription	Primary T helper cells fromperipheralblood	blood
41	chr3:51463000-51469200	Strong transcription	Primary hematopoietic stem cells	blood
42	chr3:51463000-51469400	Strong transcription	Adipose Nuclei	Adipose
43	chr3:51463000-51477200	Strong transcription	Liver	Liver
44	chr3:51463000-51477600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr3:51463200-51469200	Strong transcription	HUES48 Cell Line	embryonic stem cell
46	chr3:51463200-51470400	Strong transcription	Primary T helper cells PMA-I stimulated	--
47	chr3:51463200-51470600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
48	chr3:51463200-51471800	Strong transcription	HUES64 Cell Line	embryonic stem cell
49	chr3:51463200-51478000	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chr3:51463400-51470400	Strong transcription	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links