Variant report

Variant	rs541060333
Chromosome Location	chr3:23961055-23961056
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:26)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:26 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:23958045-23963842	GM12878	blood:	n/a	n/a
2	POLR2A	chr3:23961018-23961132	HUVEC	blood vessel:	n/a	n/a
3	POLR2A	chr3:23958006-23962277	GM12878	blood:	n/a	n/a
4	POLR2A	chr3:23957976-23965870	K562	blood:	n/a	n/a
5	POLR2A	chr3:23957870-23963941	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr3:23960634-23961089	GM12891	blood:	n/a	n/a
7	POLR2A	chr3:23960818-23964110	MCF-7	breast:	n/a	n/a
8	POLR2A	chr3:23960446-23964170	HepG2	liver:	n/a	n/a
9	POLR2A	chr3:23960601-23961078	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr3:23960417-23961072	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr3:23958113-23964020	GM12892	blood:	n/a	n/a
12	POLR2A	chr3:23960812-23963744	PFSK-1	brain:	n/a	n/a
13	CTCF	chr3:23960610-23961088	A549	lung:	n/a	n/a
14	POLR2A	chr3:23960924-23963953	U87	brain:	n/a	n/a
15	POLR2A	chr3:23960429-23961061	GM12892	blood:	n/a	n/a
16	POLR2A	chr3:23961007-23963311	U87	brain:	n/a	n/a
17	POLR2A	chr3:23960491-23963226	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr3:23961030-23964047	U87	brain:	n/a	n/a
19	POLR2A	chr3:23960676-23961079	GM12891	blood:	n/a	n/a
20	HEY1	chr3:23960507-23961061	K562	blood:	n/a	n/a
21	POLR2A	chr3:23960599-23964082	GM12892	blood:	n/a	n/a
22	POLR2A	chr3:23957988-23964598	GM12892	blood:	n/a	n/a
23	POLR2A	chr3:23960639-23961073	GM12891	blood:	n/a	n/a
24	SP1	chr3:23960600-23961182	H1-hESC	embryonic stem cell:	n/a	n/a
25	ZBTB33	chr3:23960573-23961107	K562	blood:	n/a	n/a
26	POLR2A	chr3:23957996-23961058	SK-N-MC	brain:	n/a	n/a

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:23960526..23962863-chr3:24013920..24016141,2	K562	blood:
2	chr3:23960619..23962438-chr3:24535920..24537440,2	MCF-7	breast:
3	chr3:23051768..23053551-chr3:23960276..23962039,2	K562	blood:
4	chr3:23742842..23745448-chr3:23959508..23961357,2	K562	blood:
5	chr3:23748425..23751412-chr3:23960441..23962908,2	K562	blood:
6	chr3:23960922..23962761-chr3:24002838..24004607,2	K562	blood:
7	chr3:23905396..23907030-chr3:23960105..23962888,2	K562	blood:
8	chr3:23958536..23961065-chr3:24535525..24538143,3	K562	blood:
9	chr3:23928269..23930887-chr3:23960946..23963532,2	MCF-7	breast:
10	chr3:23954505..23971330-chr3:23977357..23992645,61	MCF-7	breast:
11	chr3:12873721..12876260-chr3:23958650..23961334,2	K562	blood:
12	chr3:23845112..23848622-chr3:23958029..23961906,4	K562	blood:
13	chr3:23956631..23966740-chr3:23975650..23993173,64	MCF-7	breast:
14	chr3:23960325..23963916-chr3:24723703..24727555,4	MCF-7	breast:

No data

Variant related genes	Relation type
NKIRAS1	TF binding region
ENSG00000151090	Chromatin interaction
ENSG00000197885	Chromatin interaction
ENSG00000228791	Chromatin interaction
ENSG00000174738	Chromatin interaction
ENSG00000170142	Chromatin interaction
ENSG00000223791	Chromatin interaction
ENSG00000272263	Chromatin interaction

Extended variants
information (count: 3 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533980	chr3:23445901-24311972	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv966996	chr3:23958991-23961257	Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv1067849	chr3:23960157-23962549	Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	9 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	chr3:23958400-23961200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr3:23958800-23962000	Transcr. at gene 5' and 3'	A549	lung
3	chr3:23959000-23962000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr3:23959200-23961200	Transcr. at gene 5' and 3'	NHEK	skin
5	chr3:23959200-23961400	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
6	chr3:23959200-23961800	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr3:23959200-23961800	Transcr. at gene 5' and 3'	iPS-18 Cell Line	embryonic stem cell
8	chr3:23959200-23961800	Transcr. at gene 5' and 3'	K562	blood
9	chr3:23959200-23962000	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
10	chr3:23959400-23961200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr3:23959400-23961800	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
12	chr3:23959400-23962000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr3:23959600-23961600	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr3:23959600-23962000	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr3:23959600-23962200	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr3:23959600-23962200	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
17	chr3:23959600-23965200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr3:23959600-23965600	Weak transcription	Spleen	Spleen
19	chr3:23959600-23969400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr3:23959800-23961200	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr3:23959800-23965000	Weak transcription	Ovary	ovary
22	chr3:23960000-23961600	Weak transcription	Aorta	Aorta
23	chr3:23960000-23962000	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
24	chr3:23960000-23965000	Weak transcription	Colonic Mucosa	Colon
25	chr3:23960200-23961400	Genic enhancers	Brain Cingulate Gyrus	brain
26	chr3:23960200-23961400	Weak transcription	Gastric	stomach
27	chr3:23960200-23961600	Weak transcription	Lung	lung
28	chr3:23960200-23961600	Weak transcription	Pancreas	Pancrea
29	chr3:23960200-23961800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr3:23960200-23961800	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
31	chr3:23960200-23962000	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr3:23960200-23962000	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
33	chr3:23960200-23962000	Strong transcription	Small Intestine	intestine
34	chr3:23960200-23962200	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
35	chr3:23960200-23963000	Genic enhancers	Primary B cells from cord blood	blood
36	chr3:23960200-23964400	Strong transcription	Placenta	Placenta
37	chr3:23960200-23967000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr3:23960200-23969400	Weak transcription	Esophagus	oesophagus
39	chr3:23960400-23961400	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr3:23960400-23961400	Genic enhancers	Stomach Smooth Muscle	stomach
41	chr3:23960400-23961800	Genic enhancers	Primary T cells fromperipheralblood	blood
42	chr3:23960400-23961800	Enhancers	Fetal Heart	heart
43	chr3:23960400-23961800	Genic enhancers	Fetal Lung	lung
44	chr3:23960400-23962000	Genic enhancers	Primary B cells from peripheral blood	blood
45	chr3:23960400-23962200	Strong transcription	Primary neutrophils fromperipheralblood	blood
46	chr3:23960400-23963600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr3:23960400-23963800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr3:23960400-23963800	Strong transcription	Brain Hippocampus Middle	brain
49	chr3:23960400-23963800	Strong transcription	Thymus	Thymus
50	chr3:23960400-23964200	Strong transcription	Skeletal Muscle Male	skeletal muscle

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