Variant report

Variant	rs3913164
Chromosome Location	chr4:143394857-143394858
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:66)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:66 , 50 per page) page: 1 2

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	NR3C1	chr4:143394697-143395289	ECC-1	luminal epithelium:	n/a	n/a
3	TCF12	chr4:143394449-143396444	ECC-1	luminal epithelium:	n/a	n/a
4	CTCF	chr4:143394644-143394883	MCF-7	breast:	n/a	n/a
5	RAD21	chr4:143394544-143395054	MCF-7	breast:	n/a	n/a
6	HDAC2	chr4:143394502-143396268	MCF-7	breast:	n/a	n/a
7	SRF	chr4:143394559-143395834	ECC-1	luminal epithelium:	n/a	n/a
8	YY1	chr4:143394573-143395808	ECC-1	luminal epithelium:	n/a	n/a
9	CTCF	chr4:143394640-143394887	MCF-7	breast:	n/a	n/a
10	FOXM1	chr4:143394628-143396209	MCF-7	breast:	n/a	n/a
11	NR2F2	chr4:143394627-143396404	MCF-7	breast:	n/a	n/a
12	TEAD4	chr4:143394568-143396356	ECC-1	luminal epithelium:	n/a	n/a
13	POLR2A	chr4:143394240-143396372	MCF-7	breast:	n/a	n/a
14	MAX	chr4:143394559-143396451	ECC-1	luminal epithelium:	n/a	n/a
15	CTCF	chr4:143394720-143394870	GM12870	blood:	n/a	n/a
16	NR3C1	chr4:143394648-143395330	ECC-1	luminal epithelium:	n/a	n/a
17	EP300	chr4:143394676-143396425	MCF-7	breast:	n/a	n/a
18	NFIC	chr4:143394417-143396497	ECC-1	luminal epithelium:	n/a	n/a
19	SIN3AK20	chr4:143394688-143396246	MCF-7	breast:	n/a	n/a
20	TCF12	chr4:143394517-143396501	MCF-7	breast:	n/a	n/a
21	ESR1	chr4:143394633-143396330	ECC-1	luminal epithelium:	n/a	n/a
22	RAD21	chr4:143394498-143395231	ECC-1	luminal epithelium:	n/a	n/a
23	FOXM1	chr4:143394413-143396896	ECC-1	luminal epithelium:	n/a	n/a
24	ELF1	chr4:143394612-143396338	MCF-7	breast:	n/a	n/a
25	GATA3	chr4:143394304-143395128	MCF-7	breast:	n/a	n/a
26	CTCF	chr4:143394527-143395021	MCF-7	breast:	n/a	n/a
27	POLR2A	chr4:143394412-143396170	MCF-7	breast:	n/a	n/a
28	ESR1	chr4:143394612-143396397	ECC-1	luminal epithelium:	n/a	n/a
29	CTCF	chr4:143394720-143394870	MCF-7	breast:	n/a	n/a
30	GATA2	chr4:143394801-143395143	HUVEC	blood vessel:	n/a	n/a
31	ESR1	chr4:143394592-143396349	ECC-1	luminal epithelium:	n/a	n/a
32	POLR2A	chr4:143394700-143396277	ECC-1	luminal epithelium:	n/a	n/a
33	NR2F2	chr4:143394512-143396505	MCF-7	breast:	n/a	n/a
34	TCF12	chr4:143394357-143396599	ECC-1	luminal epithelium:	n/a	n/a
35	EP300	chr4:143394540-143396435	ECC-1	luminal epithelium:	n/a	n/a
36	CTCF	chr4:143394610-143394902	MCF-7	breast:	n/a	n/a
37	SIN3AK20	chr4:143394215-143396496	MCF-7	breast:	n/a	n/a
38	GATA3	chr4:143394172-143396432	MCF-7	breast:	n/a	n/a
39	YY1	chr4:143394435-143395354	ECC-1	luminal epithelium:	n/a	n/a
40	MAX	chr4:143394521-143396341	MCF-7	breast:	n/a	n/a
41	ESR1	chr4:143394658-143396408	ECC-1	luminal epithelium:	n/a	n/a
42	MYC	chr4:143394779-143396009	MCF-7	breast:	n/a	n/a
43	FOXA2	chr4:143394825-143395285	A549	lung:	n/a	n/a
44	NFIC	chr4:143394473-143396400	ECC-1	luminal epithelium:	n/a	n/a
45	TEAD4	chr4:143394617-143396331	ECC-1	luminal epithelium:	n/a	n/a
46	RAD21	chr4:143394443-143395021	MCF-7	breast:	n/a	n/a
47	CEBPB	chr4:143394581-143395203	ECC-1	luminal epithelium:	n/a	n/a
48	TCF12	chr4:143394575-143395305	A549	lung:	n/a	n/a
49	CTCF	chr4:143394662-143394882	MCF-7	breast:	n/a	n/a
50	FOS	chr4:143394814-143395177	HUVEC	blood vessel:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:143392966..143400087-chr4:143764739..143770446,12	MCF-7	breast:
2	chr4:143389462..143399452-chr4:143428707..143442488,28	MCF-7	breast:
3	chr4:143351692..143359150-chr4:143392769..143399702,12	MCF-7	breast:
4	chr4:143391120..143394953-chr4:143764140..143771077,8	MCF-7	breast:
5	chr4:143391421..143397876-chr4:143484529..143495051,12	MCF-7	breast:
6	chr20:46129895..46131495-chr4:143394020..143396583,2	MCF-7	breast:

No data

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

Extended variants
information (count: 51 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10008498	0.95[ASN][1000 genomes]
rs10011782	0.82[CHD][hapmap]
rs10012476	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs10015184	0.89[EUR][1000 genomes]
rs10015271	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1013397	1.00[CEU][hapmap];0.81[GIH][hapmap];0.92[TSI][hapmap];0.89[EUR][1000 genomes]
rs12643136	0.87[CEU][hapmap]
rs12644565	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs12646243	0.87[CEU][hapmap]
rs12649139	0.87[CEU][hapmap]
rs1364917	0.87[CEU][hapmap]
rs1364918	0.87[CEU][hapmap]
rs1364919	0.87[CEU][hapmap]
rs1364920	0.87[CEU][hapmap]
rs1364926	0.87[CEU][hapmap]
rs1391099	0.81[CHD][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs1425534	0.87[CEU][hapmap]
rs1425535	0.87[CEU][hapmap]
rs1425537	0.83[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs1425538	0.87[CEU][hapmap]
rs1489581	0.81[CHD][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs17016163	0.81[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs17016170	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs17016195	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17016207	0.87[CEU][hapmap]
rs17016248	0.87[CEU][hapmap];0.81[CHD][hapmap]
rs17016304	0.87[CEU][hapmap]
rs1817970	0.80[JPT][hapmap];0.81[ASN][1000 genomes]
rs2322705	1.00[CEU][hapmap];0.81[GIH][hapmap];0.92[TSI][hapmap];0.91[EUR][1000 genomes]
rs2322706	0.89[EUR][1000 genomes]
rs2322795	0.90[JPT][hapmap];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	0.86[ASW][hapmap];0.95[LWK][hapmap]
rs3913165	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4345256	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs4956444	0.91[ASN][1000 genomes]
rs6822263	0.85[CEU][hapmap]
rs7662794	0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7668133	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs7695918	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9308151	0.89[ASN][1000 genomes]
rs9308152	1.00[CEU][hapmap];0.81[GIH][hapmap];0.92[TSI][hapmap];0.88[EUR][1000 genomes]
rs931637	0.85[CEU][hapmap]
rs979511	1.00[CEU][hapmap]
rs9986090	1.00[CEU][hapmap];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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3913164	HHIP	cis	parietal	SCAN
rs3913164	INPP4B	cis	parietal	SCAN

Chromatin state (count:34 , 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	chr4:143388600-143395200	Weak transcription	HSMMtube	muscle
4	chr4:143390400-143397000	Weak transcription	Right Atrium	heart
5	chr4:143393400-143395000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr4:143394200-143395000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr4:143394200-143396400	Enhancers	Placenta	Placenta
8	chr4:143394400-143395200	Active TSS	A549	lung
9	chr4:143394400-143395600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr4:143394400-143395800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr4:143394400-143396200	Enhancers	Left Ventricle	heart
12	chr4:143394400-143396800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr4:143394600-143395200	Enhancers	Fetal Heart	heart
14	chr4:143394600-143395600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
15	chr4:143394600-143395800	Enhancers	Ovary	ovary
16	chr4:143394600-143396000	Enhancers	NHEK	skin
17	chr4:143394600-143397000	Enhancers	Primary T helper cells fromperipheralblood	blood
18	chr4:143394600-143397200	Enhancers	HMEC	breast
19	chr4:143394800-143395000	Flanking Active TSS	Stomach Mucosa	stomach
20	chr4:143394800-143395200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr4:143394800-143395400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr4:143394800-143395400	Weak transcription	Stomach Smooth Muscle	stomach
23	chr4:143394800-143395600	Flanking Active TSS	Esophagus	oesophagus
24	chr4:143394800-143395600	Strong transcription	Fetal Intestine Small	intestine
25	chr4:143394800-143395600	Enhancers	Spleen	Spleen
26	chr4:143394800-143396000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr4:143394800-143396200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr4:143394800-143396200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr4:143394800-143396200	Enhancers	Gastric	stomach
30	chr4:143394800-143396200	Enhancers	Pancreas	Pancrea
31	chr4:143394800-143396200	Enhancers	Right Ventricle	heart
32	chr4:143394800-143396400	Enhancers	Primary T cells fromperipheralblood	blood
33	chr4:143394800-143396600	Enhancers	Primary T helper cells PMA-I stimulated	--
34	chr4:143394800-143397800	Enhancers	Hela-S3	cervix

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links