Variant report

Variant	rs17016195
Chromosome Location	chr4:143396262-143396263
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:41)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:41 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GABPA	chr4:143394734-143396374	MCF-7	breast:	n/a	n/a
2	TCF12	chr4:143394449-143396444	ECC-1	luminal epithelium:	n/a	n/a
3	EP300	chr4:143395319-143396349	MCF-7	breast:	n/a	n/a
4	ZNF217	chr4:143395404-143396338	MCF-7	breast:	n/a	n/a
5	TCF7L2	chr4:143395609-143396358	MCF-7	breast:	n/a	n/a
6	GATA3	chr4:143395375-143396329	MCF-7	breast:	n/a	n/a
7	HDAC2	chr4:143394502-143396268	MCF-7	breast:	n/a	n/a
8	NR2F2	chr4:143394627-143396404	MCF-7	breast:	n/a	n/a
9	TEAD4	chr4:143394568-143396356	ECC-1	luminal epithelium:	n/a	n/a
10	ESR1	chr4:143395482-143396341	ECC-1	luminal epithelium:	n/a	n/a
11	POLR2A	chr4:143394240-143396372	MCF-7	breast:	n/a	n/a
12	MAX	chr4:143394559-143396451	ECC-1	luminal epithelium:	n/a	n/a
13	EP300	chr4:143394676-143396425	MCF-7	breast:	n/a	n/a
14	NFIC	chr4:143394417-143396497	ECC-1	luminal epithelium:	n/a	n/a
15	TCF12	chr4:143394517-143396501	MCF-7	breast:	n/a	n/a
16	ESR1	chr4:143394633-143396330	ECC-1	luminal epithelium:	n/a	n/a
17	FOXM1	chr4:143394413-143396896	ECC-1	luminal epithelium:	n/a	n/a
18	ELF1	chr4:143394612-143396338	MCF-7	breast:	n/a	n/a
19	CEBPB	chr4:143395408-143396277	MCF-7	breast:	n/a	n/a
20	ESR1	chr4:143394612-143396397	ECC-1	luminal epithelium:	n/a	n/a
21	TCF12	chr4:143395296-143396326	MCF-7	breast:	n/a	n/a
22	GATA3	chr4:143395419-143396262	T-47D	breast:	n/a	n/a
23	ESR1	chr4:143394592-143396349	ECC-1	luminal epithelium:	n/a	n/a
24	POLR2A	chr4:143394700-143396277	ECC-1	luminal epithelium:	n/a	n/a
25	NR2F2	chr4:143394512-143396505	MCF-7	breast:	n/a	n/a
26	TCF12	chr4:143394357-143396599	ECC-1	luminal epithelium:	n/a	n/a
27	EP300	chr4:143394540-143396435	ECC-1	luminal epithelium:	n/a	n/a
28	SIN3AK20	chr4:143394215-143396496	MCF-7	breast:	n/a	n/a
29	GATA3	chr4:143394172-143396432	MCF-7	breast:	n/a	n/a
30	MAX	chr4:143394521-143396341	MCF-7	breast:	n/a	n/a
31	ESR1	chr4:143394658-143396408	ECC-1	luminal epithelium:	n/a	n/a
32	NFIC	chr4:143394473-143396400	ECC-1	luminal epithelium:	n/a	n/a
33	TEAD4	chr4:143394617-143396331	ECC-1	luminal epithelium:	n/a	n/a
34	GATA3	chr4:143395355-143396503	MCF-7	breast:	n/a	n/a
35	MAX	chr4:143394555-143396362	ECC-1	luminal epithelium:	n/a	n/a
36	FOXM1	chr4:143394514-143396518	ECC-1	luminal epithelium:	n/a	n/a
37	EP300	chr4:143394324-143396569	ECC-1	luminal epithelium:	n/a	n/a
38	RAD21	chr4:143394438-143396429	ECC-1	luminal epithelium:	n/a	n/a
39	POLR2A	chr4:143394286-143396322	ECC-1	luminal epithelium:	n/a	n/a
40	ELF1	chr4:143395387-143396347	MCF-7	breast:	n/a	n/a
41	FOXM1	chr4:143395303-143396374	MCF-7	breast:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:143392966..143400087-chr4:143764739..143770446,12	MCF-7	breast:
2	chr4:143395685..143398637-chr4:143542900..143544725,2	MCF-7	breast:
3	chr4:143389462..143399452-chr4:143428707..143442488,28	MCF-7	breast:
4	chr4:143351692..143359150-chr4:143392769..143399702,12	MCF-7	breast:
5	chr4:143395976..143397476-chr4:143613237..143615113,2	MCF-7	breast:
6	chr4:143391421..143397876-chr4:143484529..143495051,12	MCF-7	breast:
7	chr20:46129895..46131495-chr4:143394020..143396583,2	MCF-7	breast:
8	chr4:143395567..143397117-chr4:143767101..143769350,2	MCF-7	breast:
9	chr4:143395579..143398506-chr4:143758143..143759826,2	MCF-7	breast:

No data

Variant related genes	Relation type
INPP4B	TF binding region
ENSG00000124151	Chromatin interaction
ENSG00000109452	Chromatin interaction
ENSG00000249806	Chromatin interaction
ENSG00000251248	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10008498	0.95[ASN][1000 genomes]
rs10012476	0.89[EUR][1000 genomes]
rs10015184	0.89[EUR][1000 genomes]
rs10015271	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1013397	0.89[EUR][1000 genomes]
rs12644565	0.89[EUR][1000 genomes]
rs1391099	0.86[ASN][1000 genomes]
rs1425537	0.83[ASN][1000 genomes]
rs1489581	0.86[ASN][1000 genomes]
rs17016163	0.88[ASN][1000 genomes]
rs17016170	0.89[EUR][1000 genomes]
rs1817970	0.81[ASN][1000 genomes]
rs2322705	0.91[EUR][1000 genomes]
rs2322706	0.89[EUR][1000 genomes]
rs2322795	0.83[ASN][1000 genomes]
rs2874841	0.90[ASN][1000 genomes]
rs28823374	0.91[EUR][1000 genomes]
rs28850298	0.91[EUR][1000 genomes]
rs28861843	0.92[EUR][1000 genomes]
rs34900920	0.91[EUR][1000 genomes]
rs3863128	0.91[ASN][1000 genomes]
rs3913163	0.90[AFR][1000 genomes]
rs3913164	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3913165	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4345256	0.91[EUR][1000 genomes]
rs4956444	0.91[ASN][1000 genomes]
rs7662794	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7668133	0.89[EUR][1000 genomes]
rs7695918	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9308151	0.89[ASN][1000 genomes]
rs9308152	0.88[EUR][1000 genomes]
rs9986090	0.85[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498005	chr4:142515689-143502988	Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:143369200-143410600	Weak transcription	Primary hematopoietic stem cells	blood
2	chr4:143371600-143400800	Weak transcription	Aorta	Aorta
3	chr4:143390400-143397000	Weak transcription	Right Atrium	heart
4	chr4:143394200-143396400	Enhancers	Placenta	Placenta
5	chr4:143394400-143396800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr4:143394600-143397000	Enhancers	Primary T helper cells fromperipheralblood	blood
7	chr4:143394600-143397200	Enhancers	HMEC	breast
8	chr4:143394800-143396400	Enhancers	Primary T cells fromperipheralblood	blood
9	chr4:143394800-143396600	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr4:143394800-143397800	Enhancers	Hela-S3	cervix
11	chr4:143395000-143396400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr4:143395000-143396400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr4:143395000-143396800	Enhancers	Primary T helper naive cells from peripheral blood	blood
14	chr4:143395000-143396800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
15	chr4:143395000-143396800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr4:143395000-143397200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr4:143395200-143396800	Flanking Active TSS	A549	lung
18	chr4:143395200-143397600	Enhancers	Muscle Satellite Cultured Cells	--
19	chr4:143395400-143396400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
20	chr4:143395400-143396400	Enhancers	Primary T killer memory cells from peripheral blood	blood
21	chr4:143395400-143403000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr4:143395600-143396400	Enhancers	Fetal Intestine Large	intestine
23	chr4:143395800-143396800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr4:143396000-143396600	Weak transcription	Fetal Intestine Small	intestine
25	chr4:143396000-143396600	Weak transcription	NH-A	brain
26	chr4:143396000-143397200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr4:143396000-143397200	Enhancers	Stomach Mucosa	stomach
28	chr4:143396200-143396800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

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