Variant report

Variant	rs3797296
Chromosome Location	chr5:52777721-52777722
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	chr5:52777611-52778241	MCF10A-Er-Src	breast:	n/a	n/a
2	EGR1	chr5:52777711-52777984	K562	blood:	n/a	chr5:52777964-52777974 chr5:52777856-52777866 chr5:52777900-52777910 chr5:52777851-52777864
3	CHD1	chr5:52773963-52779659	IMR90	lung:	n/a	chr5:52776596-52776606 chr5:52777700-52777710 chr5:52776601-52776611
4	MAZ	chr5:52777719-52778041	HepG2	liver:	n/a	chr5:52777853-52777862
5	POLR2A	chr5:52777603-52777863	SK-N-SH	brain:	n/a	n/a
6	CEBPB	chr5:52777674-52778018	HepG2	liver:	n/a	chr5:52777928-52777939
7	SIN3A	chr5:52777671-52779208	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr5:52777561-52778038	MCF10A-Er-Src	breast:	n/a	n/a
9	RAD21	chr5:52776262-52779138	IMR90	lung:	n/a	chr5:52776513-52776525 chr5:52776611-52776621
10	POLR2A	chr5:52775052-52780368	SK-N-SH	brain:	n/a	n/a
11	CHD2	chr5:52777238-52778083	Hela-S3	cervix:	n/a	chr5:52777700-52777710
12	POLR2A	chr5:52777446-52778224	U87	brain:	n/a	n/a
13	RAD21	chr5:52777643-52778079	Hela-S3	cervix:	n/a	n/a
14	RCOR1	chr5:52777710-52777987	K562	blood:	n/a	n/a
15	CEBPB	chr5:52777560-52778264	MCF-7	breast:	n/a	chr5:52777928-52777939
16	PRDM1	chr5:52777369-52777896	Hela-S3	cervix:	n/a	chr5:52777723-52777736 chr5:52777723-52777732 chr5:52777721-52777736
17	TFAP2A	chr5:52777721-52778107	Hela-S3	cervix:	n/a	chr5:52777835-52777850
18	TAF1	chr5:52777628-52777932	SK-N-SH	brain:	n/a	n/a
19	EP300	chr5:52777619-52778016	Hela-S3	cervix:	n/a	chr5:52777849-52777865
20	MAX	chr5:52777624-52778070	ECC-1	luminal epithelium:	n/a	chr5:52777853-52777862
21	MXI1	chr5:52775095-52779435	IMR90	lung:	n/a	n/a
22	CEBPB	chr5:52777707-52778124	HepG2	liver:	n/a	chr5:52777928-52777939
23	TAF1	chr5:52777600-52778071	Hela-S3	cervix:	n/a	n/a
24	POLR2A	chr5:52777626-52778075	U87	brain:	n/a	n/a
25	CEBPB	chr5:52777703-52778078	K562	blood:	n/a	chr5:52777928-52777939
26	EGR1	chr5:52777710-52777984	K562	blood:	n/a	chr5:52777964-52777974 chr5:52777856-52777866 chr5:52777900-52777910 chr5:52777851-52777864
27	POLR2A	chr5:52777674-52778149	HL-60	blood:	n/a	n/a
28	E2F6	chr5:52777539-52778183	A549	lung:	n/a	n/a
29	TFAP2C	chr5:52777661-52778144	Hela-S3	cervix:	n/a	n/a
30	HA-E2F1	chr5:52777544-52778508	MCF-7	breast:	n/a	n/a
31	UBTF	chr5:52777558-52778139	K562	blood:	n/a	n/a
32	POLR2A	chr5:52777694-52778107	HL-60	blood:	n/a	n/a
33	POLR2A	chr5:52774375-52780496	HepG2	liver:	n/a	n/a
34	POLR2A	chr5:52777639-52777991	ProgFib	skin:	n/a	n/a
35	SIN3AK20	chr5:52777637-52778079	SK-N-SH	brain:	n/a	n/a
36	MAZ	chr5:52777699-52777963	K562	blood:	n/a	chr5:52777853-52777862
37	CEBPB	chr5:52777696-52778408	IMR90	lung:	n/a	chr5:52777928-52777939 chr5:52778336-52778349
38	EBF1	chr5:52777652-52778004	GM12878	blood:	n/a	n/a
39	CEBPB	chr5:52777711-52778123	K562	blood:	n/a	chr5:52777928-52777939
40	MAX	chr5:52777695-52778039	K562	blood:	n/a	chr5:52777853-52777862
41	TAF1	chr5:52777663-52777905	Hela-S3	cervix:	n/a	n/a
42	MYC	chr5:52777590-52778092	MCF10A-Er-Src	breast:	n/a	chr5:52777853-52777862
43	GATA3	chr5:52777531-52778204	MCF-7	breast:	n/a	n/a
44	RAD21	chr5:52777644-52778097	H1-hESC	embryonic stem cell:	n/a	n/a
45	HEY1	chr5:52777494-52778109	HepG2	liver:	n/a	n/a
46	CEBPB	chr5:52777579-52778411	Hela-S3	cervix:	n/a	chr5:52777928-52777939 chr5:52778336-52778349
47	MXI1	chr5:52777658-52778050	Hela-S3	cervix:	n/a	n/a
48	TCF12	chr5:52776871-52778063	A549	lung:	n/a	n/a
49	ZKSCAN1	chr5:52777636-52777967	Hela-S3	cervix:	n/a	n/a
50	CEBPB	chr5:52777703-52778353	A549	lung:	n/a	chr5:52777928-52777939 chr5:52778336-52778349

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:52777363..52778020-chr5:53513424..53514366,2	MCF-7	breast:

Variant related genes	Relation type
FST	TF binding region

Extended variants
information (count: 9 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1423560	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2070858	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2287925	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs31305	1.00[CEU][hapmap]
rs3806901	0.93[ASN][1000 genomes]
rs9986304	0.84[CHD][hapmap]

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	nsv949005	chr5:52188028-52808229	Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	esv2752745	chr5:52422063-53343529	Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv1032632	chr5:52667145-53655624	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 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	chr5:52774200-52778200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr5:52774200-52778800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr5:52774200-52778800	Active TSS	Osteobl	bone
4	chr5:52774200-52779000	Active TSS	Colon Smooth Muscle	Colon
5	chr5:52774200-52779200	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr5:52774400-52778200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr5:52774400-52778400	Active TSS	Right Ventricle	heart
8	chr5:52774400-52778400	Bivalent/Poised TSS	Thymus	Thymus
9	chr5:52774400-52778600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr5:52774400-52778600	Active TSS	HUES6 Cell Line	embryonic stem cell
11	chr5:52774400-52778600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr5:52774400-52778600	Active TSS	Aorta	Aorta
13	chr5:52774400-52778800	Active TSS	HUES64 Cell Line	embryonic stem cell
14	chr5:52774400-52778800	Active TSS	Hela-S3	cervix
15	chr5:52774400-52778800	Active TSS	HSMM	muscle
16	chr5:52774400-52778800	Active TSS	HSMMtube	muscle
17	chr5:52774400-52778800	Active TSS	NHDF-Ad	bronchial
18	chr5:52774400-52779000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
19	chr5:52774400-52779000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr5:52774400-52779000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr5:52774400-52779000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr5:52774400-52779000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr5:52774400-52779000	Active TSS	Breast Myoepithelial Primary Cells	Breast
24	chr5:52774400-52779000	Active TSS	Gastric	stomach
25	chr5:52774400-52779000	Active TSS	Psoas Muscle	Psoas
26	chr5:52774400-52779000	Active TSS	A549	lung
27	chr5:52774400-52779200	Active TSS	H9 Cell Line	embryonic stem cell
28	chr5:52774400-52779200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr5:52774400-52779200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
30	chr5:52774400-52779400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr5:52774600-52778200	Active TSS	NHEK	skin
32	chr5:52774600-52778600	Active TSS	NHLF	lung
33	chr5:52774600-52778800	Bivalent/Poised TSS	Fetal Stomach	stomach
34	chr5:52774600-52779200	Active TSS	Rectal Smooth Muscle	rectum
35	chr5:52774800-52778400	Bivalent/Poised TSS	Fetal Muscle Trunk	muscle
36	chr5:52774800-52778600	Active TSS	HMEC	breast
37	chr5:52775000-52778800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr5:52775200-52778800	Bivalent/Poised TSS	HepG2	liver
39	chr5:52775200-52779000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr5:52775400-52778000	Active TSS	Lung	lung
41	chr5:52776000-52778200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr5:52776200-52777800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr5:52776400-52778000	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
44	chr5:52776600-52777800	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
45	chr5:52776600-52777800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr5:52776600-52777800	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
47	chr5:52776600-52777800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr5:52776600-52777800	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 29	rectum
49	chr5:52776600-52777800	Flanking Bivalent TSS/Enh	HUVEC	blood vessel
50	chr5:52776600-52777800	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links