Variant report

Variant	rs9841713
Chromosome Location	chr3:48464968-48464969
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:48464730-48464986	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr3:48461949-48470573	HepG2	liver:	n/a	n/a
3	POLR2A	chr3:48464937-48465071	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr3:48464579-48465354	HepG2	liver:	n/a	n/a
5	POLR2A	chr3:48464703-48466183	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr3:48464968-48464976	MCF-7	breast:	n/a	n/a
7	POLR2A	chr3:48464848-48465054	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr3:48463425-48465467	HepG2	liver:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:48463922..48465438-chr3:48487948..48490682,2	MCF-7	breast:
2	chr3:48459081..48461031-chr3:48464521..48467488,2	MCF-7	breast:
3	chr3:48445903..48449635-chr3:48463351..48467956,4	MCF-7	breast:
4	chr3:48458996..48461252-chr3:48463522..48466365,3	K562	blood:

No data

Variant related genes	Relation type
PLXNB1	TF binding region
ENSG00000164053	Chromatin interaction
ENSG00000164050	Chromatin interaction
ENSG00000244380	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs13325221	1.00[ASW][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[AMR][1000 genomes]
rs28789805	1.00[AMR][1000 genomes]
rs9311427	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9813424	0.89[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9815079	1.00[ASW][hapmap]
rs9823457	1.00[ASW][hapmap];1.00[MEX][hapmap]
rs9843091	0.82[LWK][hapmap];1.00[MKK][hapmap]
rs9845083	1.00[AMR][1000 genomes]
rs9867665	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834683	chr3:48301504-48493261	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	nsv834684	chr3:48385699-48589323	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv590242	chr3:48433635-48556339	Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
4	nsv876761	chr3:48464968-48496758	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription Genic enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48442000-48466200	Strong transcription	Fetal Intestine Small	intestine
2	chr3:48442000-48467400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:48442200-48466800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
4	chr3:48442600-48466600	Strong transcription	HUES48 Cell Line	embryonic stem cell
5	chr3:48443000-48467000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr3:48443200-48466400	Strong transcription	H1 Cell Line	embryonic stem cell
7	chr3:48443800-48465800	Strong transcription	Fetal Intestine Large	intestine
8	chr3:48443800-48466000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr3:48443800-48466000	Strong transcription	Fetal Brain Female	brain
10	chr3:48443800-48466400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr3:48443800-48466400	Strong transcription	Cortex derived primary cultured neurospheres	brain
12	chr3:48443800-48466600	Weak transcription	NH-A	brain
13	chr3:48444000-48465800	Strong transcription	Duodenum Mucosa	Duodenum
14	chr3:48444000-48466000	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr3:48444000-48466000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
16	chr3:48444400-48465000	Weak transcription	Fetal Brain Male	brain
17	chr3:48444400-48466000	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr3:48444400-48466200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr3:48444400-48466200	Weak transcription	Right Atrium	heart
20	chr3:48444400-48467200	Weak transcription	NHDF-Ad	bronchial
21	chr3:48444400-48468600	Weak transcription	HUVEC	blood vessel
22	chr3:48444600-48465400	Strong transcription	H9 Cell Line	embryonic stem cell
23	chr3:48444600-48465800	Strong transcription	Fetal Stomach	stomach
24	chr3:48444600-48466200	Strong transcription	Placenta Amnion	Placenta Amnion
25	chr3:48447400-48465200	Weak transcription	Fetal Heart	heart
26	chr3:48449800-48466400	Strong transcription	Rectal Mucosa Donor 29	rectum
27	chr3:48451000-48467000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr3:48451400-48466800	Weak transcription	A549	lung
29	chr3:48454200-48469000	Weak transcription	Hela-S3	cervix
30	chr3:48456600-48467600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr3:48456800-48467200	Weak transcription	Small Intestine	intestine
32	chr3:48457400-48468800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr3:48458800-48467400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr3:48459800-48468800	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr3:48460200-48466400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr3:48460400-48466000	Weak transcription	Fetal Lung	lung
37	chr3:48460600-48466600	Weak transcription	NHLF	lung
38	chr3:48461000-48465000	Weak transcription	Rectal Smooth Muscle	rectum
39	chr3:48461000-48467200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr3:48461200-48465800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr3:48462200-48466200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr3:48462400-48466200	Genic enhancers	Liver	Liver
43	chr3:48462400-48467000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr3:48462600-48469600	Enhancers	Left Ventricle	heart
45	chr3:48462800-48466000	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr3:48463000-48467000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr3:48463200-48466600	Weak transcription	Placenta	Placenta
48	chr3:48463200-48467600	Genic enhancers	Esophagus	oesophagus
49	chr3:48463400-48465000	Strong transcription	Fetal Kidney	kidney
50	chr3:48463400-48465200	Genic enhancers	NHEK	skin

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