Variant report

Variant	rs55808934
Chromosome Location	chr3:48003146-48003147
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	TEAD4	chr3:48003136-48004089	K562	blood:	n/a	n/a
2	POLR2A	chr3:48003144-48004004	K562	blood:	n/a	n/a
3	ELF1	chr3:48003029-48003568	K562	blood:	n/a	n/a
4	CUX1	chr3:48003022-48004279	K562	blood:	n/a	n/a
5	POLR2A	chr3:48003119-48003914	SK-N-MC	brain:	n/a	n/a
6	EP300	chr3:48003001-48005062	SK-N-SH	brain:	n/a	chr3:48004170-48004184 chr3:48004164-48004178

Variant related genes	Relation type
VPS26BP1	TF binding region

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1486916	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2351249	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2593817	1.00[AMR][1000 genomes]
rs319683	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34675858	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3731495	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3731539	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3731547	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4476528	1.00[AMR][1000 genomes]
rs55736379	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6442092	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6442103	1.00[EUR][1000 genomes]
rs6442104	1.00[AMR][1000 genomes]
rs6773945	1.00[AMR][1000 genomes]
rs7372108	1.00[AMR][1000 genomes]
rs73831540	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73831544	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73831562	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9863220	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9917799	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006560	chr3:47867461-48037031	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	141 gene(s)	inside rSNPs	diseases
2	nsv1011662	chr3:47891634-48019462	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv536561	chr3:47891634-48019462	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv529989	chr3:47909480-48301481	Genic enhancers Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats 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	42 gene(s)	inside rSNPs	diseases
5	nsv1001056	chr3:47912342-48223849	Genic enhancers Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	esv1796001	chr3:47912703-48012797	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	esv1826403	chr3:47912703-48012797	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	esv1835684	chr3:47912703-48123540	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
9	esv1827272	chr3:47912703-48260968	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
10	nsv1000817	chr3:47927730-48032401	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
11	nsv1009243	chr3:47935331-48340448	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
12	nsv536562	chr3:47935331-48340448	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
13	nsv1012828	chr3:47996472-48192862	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
14	nsv1002067	chr3:47996472-48326518	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription 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 miRNA target site	43 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47968600-48012600	Weak transcription	Primary B cells from cord blood	blood
2	chr3:47969200-48003200	Weak transcription	Lung	lung
3	chr3:47969800-48003200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr3:47969800-48003200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr3:47969800-48003200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr3:47969800-48004000	Weak transcription	NHLF	lung
7	chr3:47970200-48003200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:47970200-48003200	Weak transcription	Rectal Smooth Muscle	rectum
9	chr3:47970200-48013000	Weak transcription	Fetal Muscle Trunk	muscle
10	chr3:47970200-48016600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr3:47974400-48003200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr3:47974400-48012600	Weak transcription	Osteobl	bone
13	chr3:47982800-48003200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr3:47983200-48003600	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr3:47989800-48003200	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr3:47989800-48012400	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr3:47991600-48016800	Weak transcription	Fetal Intestine Large	intestine
18	chr3:47992000-48003200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr3:47992000-48003200	Weak transcription	Duodenum Mucosa	Duodenum
20	chr3:47992800-48003400	Weak transcription	A549	lung
21	chr3:47993000-48003200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr3:47994200-48003200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr3:47994200-48005400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr3:47994600-48003200	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr3:47996200-48003200	Weak transcription	Primary hematopoietic stem cells	blood
26	chr3:47996400-48018400	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr3:47996600-48014600	Weak transcription	NH-A	brain
28	chr3:47996800-48016000	Weak transcription	HUVEC	blood vessel
29	chr3:47997000-48003200	Weak transcription	Spleen	Spleen
30	chr3:47997600-48003200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr3:47997800-48003200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr3:47998200-48031400	Weak transcription	Brain Germinal Matrix	brain
33	chr3:47998400-48003200	Weak transcription	Adipose Nuclei	Adipose
34	chr3:47998400-48003200	Weak transcription	HSMM	muscle
35	chr3:47998600-48003200	Weak transcription	Fetal Muscle Leg	muscle
36	chr3:47998600-48003400	Weak transcription	Brain Angular Gyrus	brain
37	chr3:47999000-48003200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr3:48000000-48003400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr3:48001000-48007600	Weak transcription	Fetal Stomach	stomach
40	chr3:48002000-48003400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr3:48002200-48003200	Enhancers	NHEK	skin
42	chr3:48002200-48004600	Enhancers	GM12878-XiMat	blood
43	chr3:48002400-48003200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
44	chr3:48002400-48004200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
45	chr3:48002400-48005800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
46	chr3:48002400-48007400	Enhancers	HepG2	liver
47	chr3:48002600-48003200	Enhancers	Primary T helper naive cells from peripheral blood	blood
48	chr3:48002600-48003200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr3:48002600-48003400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr3:48002600-48003400	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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