Variant report

Variant	rs58840220
Chromosome Location	chr3:47016915-47016916
allele	C/T
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	chr3:47015223-47016937	GM12878	blood:	n/a	n/a
2	POLR2A	chr3:47016915-47017098	K562	blood:	n/a	n/a
3	POLR2A	chr3:47016350-47016994	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:47011340..47013025-chr3:47015501..47017285,2	MCF-7	breast:
2	chr3:47016641..47019456-chr3:47138519..47140806,2	K562	blood:

Variant related genes	Relation type
NBEAL2	TF binding region
ENSG00000181555	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10510753	0.81[AMR][1000 genomes]
rs17079331	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs17079336	0.83[AFR][1000 genomes]
rs2385870	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs4515087	0.81[AMR][1000 genomes]
rs57246717	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs57313197	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs59295935	0.89[AFR][1000 genomes]
rs59321380	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6442051	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72905877	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs72905900	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs72907932	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs72907946	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7612808	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs7632511	0.84[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv536558	chr3:46706571-47024756	Enhancers Bivalent Enhancer Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	nsv876755	chr3:46895109-47061183	Genic enhancers Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	esv3461834	chr3:46977730-47173228	Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	esv3461835	chr3:46977822-47173168	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	esv3461836	chr3:46977822-47173168	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	nsv1009396	chr3:46994991-47048166	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv876756	chr3:47002931-47586514	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
8	esv1800172	chr3:47013346-47049306	Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
9	esv3416192	chr3:47014913-47017316	Weak transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47004800-47017200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr3:47004800-47017200	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr3:47006600-47017000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
4	chr3:47007000-47017400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr3:47007200-47017400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:47007600-47017200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr3:47007600-47017200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr3:47007600-47017400	Weak transcription	HSMMtube	muscle
9	chr3:47009200-47017200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr3:47011200-47017200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr3:47011200-47017200	Weak transcription	Aorta	Aorta
12	chr3:47012800-47017200	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr3:47013200-47017400	Weak transcription	Fetal Kidney	kidney
14	chr3:47013400-47017200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr3:47013400-47017200	Weak transcription	Esophagus	oesophagus
16	chr3:47013400-47017400	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr3:47013400-47017400	Weak transcription	Brain Substantia Nigra	brain
18	chr3:47013600-47017200	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr3:47013800-47017200	Weak transcription	Fetal Stomach	stomach
20	chr3:47013800-47017400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr3:47014600-47017200	Enhancers	Small Intestine	intestine
22	chr3:47015200-47017200	Enhancers	Primary T cells from cord blood	blood
23	chr3:47015200-47017200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr3:47015200-47017200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
25	chr3:47015200-47017200	Enhancers	Lung	lung
26	chr3:47015200-47017400	Enhancers	Primary T killer memory cells from peripheral blood	blood
27	chr3:47015400-47017400	Enhancers	Primary neutrophils fromperipheralblood	blood
28	chr3:47015400-47017400	Enhancers	Skeletal Muscle Female	skeletal muscle
29	chr3:47015400-47017800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
30	chr3:47015600-47017200	Enhancers	Brain Inferior Temporal Lobe	brain
31	chr3:47015600-47017200	Enhancers	Colonic Mucosa	Colon
32	chr3:47015600-47017200	Enhancers	Sigmoid Colon	Sigmoid Colon
33	chr3:47015600-47017200	Enhancers	Skeletal Muscle Male	skeletal muscle
34	chr3:47015800-47017000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr3:47015800-47017000	Flanking Active TSS	Liver	Liver
36	chr3:47015800-47017000	Enhancers	Placenta	Placenta
37	chr3:47015800-47017200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
38	chr3:47015800-47017200	Enhancers	Brain Germinal Matrix	brain
39	chr3:47015800-47017200	Enhancers	Ovary	ovary
40	chr3:47015800-47017200	Enhancers	Pancreas	Pancrea
41	chr3:47015800-47017400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
42	chr3:47016000-47017000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
43	chr3:47016000-47017000	Transcr. at gene 5' and 3'	K562	blood
44	chr3:47016000-47017200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr3:47016000-47018600	Active TSS	GM12878-XiMat	blood
46	chr3:47016200-47017000	Flanking Active TSS	HUVEC	blood vessel
47	chr3:47016200-47017200	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr3:47016200-47017200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr3:47016200-47017200	Weak transcription	Right Atrium	heart
50	chr3:47016200-47018000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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