Variant report

Variant	rs16854752
Chromosome Location	chr3:143689684-143689685
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	ZBTB7A	chr3:143689675-143691051	ECC-1	luminal epithelium:	n/a	n/a
2	POLR2A	chr3:143689636-143692179	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr3:143689448-143692708	HUVEC	blood vessel:	n/a	n/a
4	REST	chr3:143689428-143691555	H1-neurons	neurons:	n/a	chr3:143689885-143689905 chr3:143689912-143689925
5	TCF7L2	chr3:143689631-143692487	HCT-116	colon:	n/a	n/a
6	MAX	chr3:143689475-143692453	A549	lung:	n/a	chr3:143689817-143689826 chr3:143689829-143689838 chr3:143689513-143689522
7	POLR2A	chr3:143689516-143692415	HL-60	blood:	n/a	n/a
8	MAX	chr3:143689667-143692276	ECC-1	luminal epithelium:	n/a	chr3:143689817-143689826 chr3:143689829-143689838
9	ATF2	chr3:143689546-143689945	GM12878	blood:	n/a	n/a
10	MYC	chr3:143689557-143692334	K562	blood:	n/a	chr3:143689817-143689826 chr3:143689829-143689838
11	FOXM1	chr3:143689578-143692479	GM12878	blood:	n/a	n/a
12	POLR2A	chr3:143689635-143692573	GM12878	blood:	n/a	n/a
13	MAX	chr3:143689459-143692886	Hela-S3	cervix:	n/a	chr3:143689817-143689826 chr3:143689829-143689838 chr3:143689513-143689522
14	POLR2A	chr3:143689651-143692557	GM18526	blood:	n/a	n/a
15	MYC	chr3:143689633-143692296	K562	blood:	n/a	chr3:143689817-143689826 chr3:143689829-143689838
16	MAX	chr3:143689528-143692416	HCT-116	colon:	n/a	chr3:143689817-143689826 chr3:143689829-143689838
17	POLR2A	chr3:143689670-143692495	GM15510	blood:	n/a	n/a
18	MXI1	chr3:143689654-143692425	GM12878	blood:	n/a	chr3:143689823-143689838 chr3:143689811-143689826
19	MAX	chr3:143689675-143691869	A549	lung:	n/a	chr3:143689817-143689826 chr3:143689829-143689838
20	CREB1	chr3:143689619-143691129	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr3:143689673-143690038	GM12878	blood:	n/a	n/a
22	MXI1	chr3:143689589-143692923	Hela-S3	cervix:	n/a	chr3:143689823-143689838 chr3:143689811-143689826 chr3:143689595-143689604
23	MYC	chr3:143689554-143692333	NB4	blood:	n/a	chr3:143689817-143689826 chr3:143689829-143689838
24	SIN3AK20	chr3:143689603-143691944	MCF-7	breast:	n/a	n/a
25	EBF1	chr3:143689546-143691654	GM12878	blood:	n/a	n/a
26	HA-E2F1	chr3:143689572-143692533	MCF-7	breast:	n/a	chr3:143690620-143690629 chr3:143690586-143690595 chr3:143690818-143690827 chr3:143690784-143690794 chr3:143691005-143691017
27	ATF2	chr3:143689642-143689972	H1-hESC	embryonic stem cell:	n/a	n/a
28	ELF1	chr3:143689654-143692414	GM12878	blood:	n/a	chr3:143691041-143691053 chr3:143690785-143690797
29	MYC	chr3:143689581-143692797	K562	blood:	n/a	chr3:143689817-143689826 chr3:143689829-143689838
30	POLR2A	chr3:143689567-143692266	NB4	blood:	n/a	n/a
31	ZNF263	chr3:143689537-143692886	HEK293-T-REx	kidney:	n/a	chr3:143690863-143690884 chr3:143690386-143690395
32	PML	chr3:143689523-143692462	GM12878	blood:	n/a	chr3:143689898-143689906
33	E2F6	chr3:143689668-143692237	K562	blood:	n/a	chr3:143690620-143690629 chr3:143690586-143690595 chr3:143690818-143690827 chr3:143690784-143690794 chr3:143691005-143691017
34	ELK1	chr3:143689556-143690953	GM12878	blood:	n/a	n/a
35	POLR2A	chr3:143689532-143692596	Raji	blood:	n/a	n/a
36	POLR2A	chr3:143689663-143692547	K562	blood:	n/a	n/a
37	POLR2A	chr3:143689444-143691646	MCF10A-Er-Src	breast:	n/a	n/a
38	POLR2A	chr3:143689585-143691926	H1-hESC	embryonic stem cell:	n/a	n/a
39	USF2	chr3:143689660-143689829	H1-hESC	embryonic stem cell:	n/a	n/a
40	RELA	chr3:143689556-143692832	GM12891	blood:	n/a	n/a
41	SMARCB1	chr3:143689622-143692816	Hela-S3	cervix:	n/a	n/a
42	POLR2A	chr3:143689627-143692177	H1-hESC	embryonic stem cell:	n/a	n/a
43	POLR2A	chr3:143689661-143691222	U87	brain:	n/a	n/a
44	CHD2	chr3:143689674-143692871	Hela-S3	cervix:	n/a	chr3:143690321-143690331 chr3:143690247-143690257
45	MAX	chr3:143689549-143692435	MCF-7	breast:	n/a	chr3:143689817-143689826 chr3:143689829-143689838
46	YY1	chr3:143689674-143690015	K562	blood:	n/a	n/a
47	SIN3A	chr3:143689593-143692851	H1-hESC	embryonic stem cell:	n/a	chr3:143691988-143692001
48	MAX	chr3:143689625-143691790	HUVEC	blood vessel:	n/a	chr3:143689817-143689826 chr3:143689829-143689838
49	YY1	chr3:143689603-143690415	H1-hESC	embryonic stem cell:	n/a	n/a
50	E2F6	chr3:143689680-143690056	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:12956339..12957122-chr3:143689535..143690489,2	Hela-S3	cervix:
2	chr3:143688929..143690453-chr9:116724811..116727064,2	MCF-7	breast:
3	chr17:57914617..57916585-chr3:143689584..143691332,2	MCF-7	breast:

Variant related genes	Relation type
C3orf58	TF binding region
ENSG00000062716	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs28475588	1.00[AMR][1000 genomes]
rs56805765	1.00[AMR][1000 genomes]
rs57432713	1.00[AMR][1000 genomes]
rs73870585	0.90[AFR][1000 genomes]
rs73870586	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73870587	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73870994	1.00[AMR][1000 genomes]
rs73872624	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73872667	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7623588	0.85[AFR][1000 genomes]
rs7643008	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][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	nsv877568	chr3:143621140-143992630	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	esv3365190	chr3:143642195-143925886	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv591922	chr3:143645242-143825439	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv518814	chr3:143666825-143703750	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	31 gene(s)	inside rSNPs	diseases
5	esv3349108	chr3:143676303-143692796	Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	31 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	chr3:143688800-143696400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr3:143689000-143693200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:143689000-143694400	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr3:143689000-143695400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
5	chr3:143689000-143696800	Active TSS	Stomach Smooth Muscle	stomach
6	chr3:143689200-143689800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr3:143689200-143690000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr3:143689200-143693200	Active TSS	A549	lung
9	chr3:143689200-143693400	Active TSS	iPS-20b Cell Line	embryonic stem cell
10	chr3:143689200-143693800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr3:143689200-143694400	Active TSS	HUES48 Cell Line	embryonic stem cell
12	chr3:143689200-143695400	Active TSS	K562	blood
13	chr3:143689200-143695800	Active TSS	HUES6 Cell Line	embryonic stem cell
14	chr3:143689200-143696200	Active TSS	GM12878-XiMat	blood
15	chr3:143689400-143689800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
16	chr3:143689400-143689800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
17	chr3:143689400-143689800	Flanking Active TSS	Primary B cells from peripheral blood	blood
18	chr3:143689400-143689800	Flanking Active TSS	Primary hematopoietic stem cells	blood
19	chr3:143689400-143689800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
20	chr3:143689400-143689800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr3:143689400-143689800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
22	chr3:143689400-143689800	Flanking Active TSS	Adipose Nuclei	Adipose
23	chr3:143689400-143689800	Flanking Active TSS	Fetal Lung	lung
24	chr3:143689400-143689800	Flanking Active TSS	Hela-S3	cervix
25	chr3:143689400-143689800	Flanking Active TSS	HSMMtube	muscle
26	chr3:143689400-143689800	Flanking Active TSS	HUVEC	blood vessel
27	chr3:143689400-143689800	Flanking Active TSS	NH-A	brain
28	chr3:143689400-143689800	Flanking Active TSS	NHEK	skin
29	chr3:143689400-143690000	Flanking Active TSS	Primary B cells from cord blood	blood
30	chr3:143689400-143690000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
31	chr3:143689400-143690000	Flanking Active TSS	HMEC	breast
32	chr3:143689400-143690200	Flanking Active TSS	Dnd41	blood
33	chr3:143689400-143690600	Active TSS	Brain Germinal Matrix	brain
34	chr3:143689400-143691000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr3:143689400-143691200	Active TSS	Skeletal Muscle Female	skeletal muscle
36	chr3:143689400-143691400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr3:143689400-143692000	Active TSS	Placenta	Placenta
38	chr3:143689400-143692400	Active TSS	Primary T cells from cord blood	blood
39	chr3:143689400-143692400	Active TSS	Duodenum Mucosa	Duodenum
40	chr3:143689400-143692600	Active TSS	Primary T helper naive cells from peripheral blood	blood
41	chr3:143689400-143693000	Active TSS	Fetal Kidney	kidney
42	chr3:143689400-143693200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
43	chr3:143689400-143693200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr3:143689400-143693200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr3:143689400-143693200	Active TSS	Rectal Mucosa Donor 29	rectum
46	chr3:143689400-143693200	Active TSS	Stomach Mucosa	stomach
47	chr3:143689400-143693400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr3:143689400-143693400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr3:143689400-143693400	Active TSS	Colon Smooth Muscle	Colon
50	chr3:143689400-143693400	Active TSS	Psoas Muscle	Psoas

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links