Variant report

Variant	rs1387005
Chromosome Location	chr3:48651891-48651892
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	JUND	chr3:48651475-48652020	Hela-S3	cervix:	n/a	chr3:48651760-48651771
2	RAD21	chr3:48651591-48651917	Hela-S3	cervix:	n/a	n/a
3	STAT3	chr3:48651556-48652015	Hela-S3	cervix:	n/a	n/a
4	JUND	chr3:48651576-48651947	HepG2	liver:	n/a	chr3:48651760-48651771
5	RCOR1	chr3:48651571-48651985	Hela-S3	cervix:	n/a	n/a
6	CEBPB	chr3:48651538-48651956	IMR90	lung:	n/a	chr3:48651743-48651754
7	CEBPB	chr3:48651604-48651989	A549	lung:	n/a	chr3:48651743-48651754
8	STAT3	chr3:48651538-48651942	MCF10A-Er-Src	breast:	n/a	n/a
9	JUN	chr3:48651597-48651938	HepG2	liver:	n/a	n/a
10	FOS	chr3:48651501-48652008	MCF10A-Er-Src	breast:	n/a	chr3:48651760-48651771
11	CEBPB	chr3:48651521-48652016	Hela-S3	cervix:	n/a	chr3:48651743-48651754
12	SMC3	chr3:48651556-48652030	Hela-S3	cervix:	n/a	n/a
13	STAT3	chr3:48651538-48651996	MCF10A-Er-Src	breast:	n/a	n/a
14	JUN	chr3:48651609-48651926	HUVEC	blood vessel:	n/a	n/a
15	MYC	chr3:48651582-48651939	MCF10A-Er-Src	breast:	n/a	n/a
16	FOS	chr3:48651541-48651968	MCF10A-Er-Src	breast:	n/a	chr3:48651760-48651771
17	CHD2	chr3:48651543-48651933	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr3:48651454-48651950	Hela-S3	cervix:	n/a	n/a
19	STAT3	chr3:48651580-48651924	MCF10A-Er-Src	breast:	n/a	n/a
20	EP300	chr3:48651517-48652005	Hela-S3	cervix:	n/a	n/a
21	MYC	chr3:48651600-48651986	MCF10A-Er-Src	breast:	n/a	n/a
22	FOS	chr3:48651556-48651996	MCF10A-Er-Src	breast:	n/a	chr3:48651760-48651771
23	TBP	chr3:48651480-48651999	Hela-S3	cervix:	n/a	n/a
24	FOS	chr3:48651551-48651996	MCF10A-Er-Src	breast:	n/a	chr3:48651760-48651771
25	CEBPB	chr3:48651571-48651915	A549	lung:	n/a	chr3:48651743-48651754
26	POLR2A	chr3:48651580-48651959	MCF10A-Er-Src	breast:	n/a	n/a
27	JUN	chr3:48651480-48651963	Hela-S3	cervix:	n/a	n/a
28	GTF2F1	chr3:48651550-48652005	Hela-S3	cervix:	n/a	n/a
29	CEBPB	chr3:48651560-48651920	HepG2	liver:	n/a	chr3:48651743-48651754
30	STAT3	chr3:48651586-48651932	MCF10A-Er-Src	breast:	n/a	n/a
31	ARID3A	chr3:48651616-48651952	HepG2	liver:	n/a	n/a
32	FOS	chr3:48651475-48651994	HUVEC	blood vessel:	n/a	chr3:48651760-48651771

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:48650192..48651894-chr3:48699672..48702339,2	MCF-7	breast:

Variant related genes	Relation type
UQCRC1	TF binding region
ENSG00000228350	Chromatin interaction
ENSG00000008300	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs59643945	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs61368683	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6800132	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9833600	1.00[ASW][hapmap];0.96[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9839959	0.90[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9866124	0.89[ASW][hapmap];0.93[LWK][hapmap];0.81[MKK][hapmap];0.86[YRI][hapmap];0.91[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008232	chr3:48517121-48702416	Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv523981	chr3:48520289-48721040	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv834685	chr3:48565009-48745774	Strong transcription Active TSS Genic enhancers Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
4	nsv876762	chr3:48591481-48731487	Strong transcription Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
5	nsv818138	chr3:48610925-48731487	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	nsv590246	chr3:48628014-48721040	Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48647400-48653600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:48647400-48654600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr3:48647400-48654600	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr3:48647400-48654800	Weak transcription	Gastric	stomach
5	chr3:48647600-48654600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr3:48648200-48652600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr3:48648400-48654600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr3:48648400-48661200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr3:48648600-48652400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr3:48648600-48653400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr3:48648600-48653400	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr3:48648600-48653400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr3:48648600-48654600	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr3:48648600-48654600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr3:48648800-48653600	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr3:48649000-48672000	Weak transcription	Fetal Brain Male	brain
17	chr3:48649200-48652600	Enhancers	HepG2	liver
18	chr3:48650600-48653400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr3:48651000-48652000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr3:48651000-48652400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr3:48651000-48652600	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr3:48651000-48652800	Enhancers	Placenta	Placenta
23	chr3:48651200-48652000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr3:48651200-48652000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr3:48651200-48652000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
26	chr3:48651200-48652000	Enhancers	HUVEC	blood vessel
27	chr3:48651200-48652000	Enhancers	NHDF-Ad	bronchial
28	chr3:48651200-48652200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
29	chr3:48651200-48652200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr3:48651200-48652200	Enhancers	NHEK	skin
31	chr3:48651200-48652200	Enhancers	Osteobl	bone
32	chr3:48651200-48652400	Enhancers	HMEC	breast
33	chr3:48651400-48652000	Strong transcription	H9 Cell Line	embryonic stem cell
34	chr3:48651400-48652000	Flanking Active TSS	Hela-S3	cervix
35	chr3:48651400-48652200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr3:48651400-48652200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr3:48651400-48652200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr3:48651600-48652000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr3:48651600-48652000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr3:48651600-48652000	Enhancers	NH-A	brain
41	chr3:48651800-48652000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr3:48651800-48652000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
43	chr3:48651800-48652000	Strong transcription	Dnd41	blood
44	chr3:48651800-48652000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
45	chr3:48651800-48662400	Weak transcription	NHLF	lung

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