Variant report

Variant	rs3913163
Chromosome Location	chr4:143394613-143394614
allele	G/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:7)
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	TCF12	chr4:143394449-143396444	ECC-1	luminal epithelium:	n/a	n/a
2	RAD21	chr4:143394544-143395054	MCF-7	breast:	n/a	n/a
3	HDAC2	chr4:143394502-143396268	MCF-7	breast:	n/a	n/a
4	SRF	chr4:143394559-143395834	ECC-1	luminal epithelium:	n/a	n/a
5	CTCF	chr4:143394600-143394750	RPTEC	kidney:	n/a	n/a
6	YY1	chr4:143394573-143395808	ECC-1	luminal epithelium:	n/a	n/a
7	TEAD4	chr4:143394568-143396356	ECC-1	luminal epithelium:	n/a	n/a
8	POLR2A	chr4:143394240-143396372	MCF-7	breast:	n/a	n/a
9	MAX	chr4:143394559-143396451	ECC-1	luminal epithelium:	n/a	n/a
10	NFIC	chr4:143394417-143396497	ECC-1	luminal epithelium:	n/a	n/a
11	TCF12	chr4:143394517-143396501	MCF-7	breast:	n/a	n/a
12	RAD21	chr4:143394498-143395231	ECC-1	luminal epithelium:	n/a	n/a
13	FOXM1	chr4:143394413-143396896	ECC-1	luminal epithelium:	n/a	n/a
14	ELF1	chr4:143394612-143396338	MCF-7	breast:	n/a	n/a
15	GATA3	chr4:143394304-143395128	MCF-7	breast:	n/a	n/a
16	CTCF	chr4:143394527-143395021	MCF-7	breast:	n/a	n/a
17	POLR2A	chr4:143394412-143396170	MCF-7	breast:	n/a	n/a
18	ESR1	chr4:143394612-143396397	ECC-1	luminal epithelium:	n/a	n/a
19	ESR1	chr4:143394592-143396349	ECC-1	luminal epithelium:	n/a	n/a
20	NR2F2	chr4:143394512-143396505	MCF-7	breast:	n/a	n/a
21	TCF12	chr4:143394357-143396599	ECC-1	luminal epithelium:	n/a	n/a
22	EP300	chr4:143394540-143396435	ECC-1	luminal epithelium:	n/a	n/a
23	CTCF	chr4:143394610-143394902	MCF-7	breast:	n/a	n/a
24	SIN3AK20	chr4:143394215-143396496	MCF-7	breast:	n/a	n/a
25	GATA3	chr4:143394172-143396432	MCF-7	breast:	n/a	n/a
26	YY1	chr4:143394435-143395354	ECC-1	luminal epithelium:	n/a	n/a
27	MAX	chr4:143394521-143396341	MCF-7	breast:	n/a	n/a
28	NFIC	chr4:143394473-143396400	ECC-1	luminal epithelium:	n/a	n/a
29	RAD21	chr4:143394443-143395021	MCF-7	breast:	n/a	n/a
30	CEBPB	chr4:143394581-143395203	ECC-1	luminal epithelium:	n/a	n/a
31	TCF12	chr4:143394575-143395305	A549	lung:	n/a	n/a
32	PML	chr4:143394339-143396121	MCF-7	breast:	n/a	n/a
33	CEBPB	chr4:143394559-143395801	ECC-1	luminal epithelium:	n/a	n/a
34	MAFK	chr4:143394477-143394624	HepG2	liver:	n/a	chr4:143394513-143394528
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	GATA3	chr4:143393961-143395342	MCF-7	breast:	n/a	n/a
40	CEBPB	chr4:143394587-143395017	MCF-7	breast:	n/a	n/a
41	POLR2A	chr4:143394286-143396322	ECC-1	luminal epithelium:	n/a	n/a

No data

(count:7 , 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	chr4:143392466..143394692-chr4:143481340..143483349,2	MCF-7	breast:
5	chr4:143391120..143394953-chr4:143764140..143771077,8	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:

No data

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

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10008498	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10011782	0.92[CEU][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.80[TSI][hapmap];0.85[AMR][1000 genomes]
rs12108640	0.85[AMR][1000 genomes]
rs1391099	1.00[CEU][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1425531	0.92[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.85[AMR][1000 genomes]
rs1425533	0.92[CEU][hapmap];0.81[TSI][hapmap]
rs1425536	0.92[CEU][hapmap]
rs1425537	0.92[CEU][hapmap];0.85[AMR][1000 genomes]
rs1489581	1.00[CEU][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1593360	0.89[JPT][hapmap]
rs17016163	1.00[CEU][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17016175	1.00[CEU][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.81[YRI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17016195	0.90[AFR][1000 genomes]
rs17016233	0.83[JPT][hapmap]
rs17016306	0.92[CEU][hapmap];0.82[GIH][hapmap];0.81[TSI][hapmap]
rs1817970	0.92[CEU][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1834391	0.88[AMR][1000 genomes]
rs2113997	0.92[CEU][hapmap];0.81[TSI][hapmap]
rs2322795	0.92[CEU][hapmap];0.92[AMR][1000 genomes]
rs2874841	0.85[AMR][1000 genomes]
rs2874865	0.85[AMR][1000 genomes]
rs28822497	0.85[AMR][1000 genomes]
rs3844178	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3863128	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3913164	0.86[ASW][hapmap];0.95[LWK][hapmap]
rs4956444	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4975308	0.91[AMR][1000 genomes]
rs6837163	0.94[JPT][hapmap]
rs713071	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7662794	0.90[AFR][1000 genomes]
rs7672965	1.00[CEU][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes]
rs9308151	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs976564	0.85[AMR][1000 genomes]
rs979511	0.84[MEX][hapmap]

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:24 , 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	chr4:143380400-143394800	Weak transcription	Pancreas	Pancrea
4	chr4:143384600-143394800	Weak transcription	Fetal Intestine Small	intestine
5	chr4:143385200-143394800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr4:143388600-143395200	Weak transcription	HSMMtube	muscle
7	chr4:143390400-143397000	Weak transcription	Right Atrium	heart
8	chr4:143393400-143395000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr4:143394200-143395000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr4:143394200-143396400	Enhancers	Placenta	Placenta
11	chr4:143394400-143394800	Enhancers	Stomach Smooth Muscle	stomach
12	chr4:143394400-143395200	Active TSS	A549	lung
13	chr4:143394400-143395600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr4:143394400-143395800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr4:143394400-143396200	Enhancers	Left Ventricle	heart
16	chr4:143394400-143396800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr4:143394600-143394800	Active TSS	Esophagus	oesophagus
18	chr4:143394600-143394800	Enhancers	Stomach Mucosa	stomach
19	chr4:143394600-143395200	Enhancers	Fetal Heart	heart
20	chr4:143394600-143395600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
21	chr4:143394600-143395800	Enhancers	Ovary	ovary
22	chr4:143394600-143396000	Enhancers	NHEK	skin
23	chr4:143394600-143397000	Enhancers	Primary T helper cells fromperipheralblood	blood
24	chr4:143394600-143397200	Enhancers	HMEC	breast

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