Variant report

Variant	rs253061
Chromosome Location	chr5:76014000-76014001
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	chr5:76011041-76015191	HUVEC	blood vessel:	n/a	n/a
2	GATA2	chr5:76013980-76014865	HUVEC	blood vessel:	n/a	chr5:76014400-76014410
3	POLR2A	chr5:76013477-76014492	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr5:76013221-76014457	SK-N-SH	brain:	n/a	n/a
5	POLR2A	chr5:76010938-76016234	HUVEC	blood vessel:	n/a	n/a
6	POLR2A	chr5:76011173-76015204	SK-N-SH	brain:	n/a	n/a
7	POLR2A	chr5:76011096-76014987	HUVEC	blood vessel:	n/a	n/a
8	POLR2A	chr5:76011442-76014817	IMR90	lung:	n/a	n/a
9	POLR2A	chr5:76010859-76015123	HUVEC	blood vessel:	n/a	n/a
10	POLR2A	chr5:76013485-76014039	GM12878	blood:	n/a	n/a
11	POLR2A	chr5:76010957-76015172	HUVEC	blood vessel:	n/a	n/a

Variant related genes	Relation type
ENSG00000225407	TF binding region

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs153311	0.80[TSI][hapmap]
rs27135	0.80[CHB][hapmap];0.90[CHD][hapmap];0.82[ASN][1000 genomes]
rs27593	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.94[LWK][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs27950	0.89[EUR][1000 genomes]
rs37242	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs37243	0.86[ASN][1000 genomes]
rs37244	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs37245	0.89[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs37246	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs37248	0.89[CHB][hapmap];0.92[CHD][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs37249	0.93[JPT][hapmap]
rs463188	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1019669	chr5:75836365-76477788	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Active 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	33 gene(s)	inside rSNPs	diseases
2	nsv1035135	chr5:75927027-76092058	Strong transcription Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv882207	chr5:75997213-76027823	Bivalent Enhancer Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv882208	chr5:75997213-76034355	Active TSS Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv882209	chr5:76004933-76034355	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:76010400-76015000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr5:76010600-76014200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr5:76011200-76014400	Active TSS	Fetal Kidney	kidney
4	chr5:76011600-76014200	Active TSS	Fetal Brain Female	brain
5	chr5:76011800-76014200	Active TSS	Fetal Intestine Large	intestine
6	chr5:76012200-76014000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
7	chr5:76012400-76014800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr5:76012800-76014000	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr5:76012800-76014400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr5:76012800-76014400	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
11	chr5:76012800-76014800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr5:76012800-76018000	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr5:76013000-76014000	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
14	chr5:76013000-76014000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr5:76013000-76014000	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
16	chr5:76013000-76014000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr5:76013000-76014000	Enhancers	Fetal Heart	heart
18	chr5:76013000-76014000	Flanking Active TSS	Fetal Lung	lung
19	chr5:76013000-76014000	Weak transcription	Small Intestine	intestine
20	chr5:76013000-76014200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr5:76013000-76014400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr5:76013000-76014800	Weak transcription	Spleen	Spleen
23	chr5:76013000-76028400	Weak transcription	Aorta	Aorta
24	chr5:76013000-76032000	Weak transcription	HSMM	muscle
25	chr5:76013000-76033000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr5:76013200-76014000	Flanking Active TSS	NH-A	brain
27	chr5:76013200-76014200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr5:76013200-76014400	Enhancers	HepG2	liver
29	chr5:76013400-76014000	Enhancers	H9 Cell Line	embryonic stem cell
30	chr5:76013400-76014000	Active TSS	Fetal Intestine Small	intestine
31	chr5:76013400-76014000	Transcr. at gene 5' and 3'	HUVEC	blood vessel
32	chr5:76013400-76014000	Flanking Active TSS	K562	blood
33	chr5:76013400-76014200	Flanking Active TSS	Brain Germinal Matrix	brain
34	chr5:76013400-76014400	Flanking Active TSS	Osteobl	bone
35	chr5:76013400-76014800	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr5:76013400-76017400	Enhancers	Primary T cells fromperipheralblood	blood
37	chr5:76013400-76017600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
38	chr5:76013400-76020000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr5:76013600-76014000	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr5:76013600-76014000	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr5:76013600-76014000	Flanking Active TSS	Fetal Brain Male	brain
42	chr5:76013600-76014000	Flanking Active TSS	Fetal Muscle Leg	muscle
43	chr5:76013600-76014000	Flanking Active TSS	Fetal Stomach	stomach
44	chr5:76013600-76014400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr5:76013600-76014400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr5:76013600-76014800	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr5:76013600-76015000	Transcr. at gene 5' and 3'	NHLF	lung
48	chr5:76013600-76016800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr5:76013800-76014000	Active TSS	HUES48 Cell Line	embryonic stem cell
50	chr5:76013800-76014000	Active TSS	HUES6 Cell Line	embryonic stem cell

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