Variant report

Variant	rs73260579
Chromosome Location	chr5:114962471-114962472
allele	A/C
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	chr5:114959884-114962471	GM12891	blood:	n/a	n/a
2	POLR2A	chr5:114960986-114962579	IMR90	lung:	n/a	n/a
3	ZKSCAN1	chr5:114961279-114962486	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr5:114961161-114962673	HepG2	liver:	n/a	n/a
5	POLR2A	chr5:114961185-114962598	Raji	blood:	n/a	n/a
6	REST	chr5:114960950-114962674	H1-neurons	neurons:	n/a	n/a
7	ZNF384	chr5:114961223-114962493	K562	blood:	n/a	n/a
8	MAX	chr5:114961116-114962499	HepG2	liver:	n/a	n/a
9	MYC	chr5:114961213-114962472	NB4	blood:	n/a	n/a
10	MAX	chr5:114961200-114962564	NB4	blood:	n/a	n/a
11	SMC3	chr5:114961561-114962544	Hela-S3	cervix:	n/a	n/a
12	SIN3A	chr5:114961102-114962486	GM12878	blood:	n/a	n/a
13	RFX5	chr5:114962199-114962621	K562	blood:	n/a	n/a
14	MYC	chr5:114961475-114962498	A549	lung:	n/a	n/a
15	CUX1	chr5:114961609-114962641	K562	blood:	n/a	chr5:114962193-114962207
16	POLR2A	chr5:114961118-114962583	Hela-S3	cervix:	n/a	n/a
17	TAL1	chr5:114961630-114962497	K562	blood:	n/a	n/a
18	SP1	chr5:114961324-114962501	HCT-116	colon:	n/a	chr5:114961750-114961762 chr5:114961874-114961884 chr5:114961870-114961884 chr5:114961874-114961883 chr5:114961875-114961884 chr5:114961920-114961930 chr5:114961750-114961762 chr5:114961875-114961884 chr5:114961874-114961884 chr5:114961752-114961761 chr5:114961747-114961761 chr5:114961873-114961885 chr5:114961873-114961885
19	EP300	chr5:114961307-114962651	K562	blood:	n/a	chr5:114961929-114961938
20	ARID3A	chr5:114961632-114962498	K562	blood:	n/a	n/a
21	SIN3AK20	chr5:114961004-114962625	MCF-7	breast:	n/a	n/a
22	POLR2A	chr5:114961135-114962597	PFSK-1	brain:	n/a	n/a
23	ZNF143	chr5:114961541-114962485	K562	blood:	n/a	chr5:114961861-114961879 chr5:114961735-114961753 chr5:114961856-114961875
24	TRIM28	chr5:114961576-114962521	K562	blood:	n/a	n/a
25	CEBPB	chr5:114961718-114962500	K562	blood:	n/a	n/a
26	TBP	chr5:114961522-114962529	GM12878	blood:	n/a	n/a
27	POLR2A	chr5:114961283-114962662	HCT-116	colon:	n/a	n/a
28	POLR2A	chr5:114961264-114962518	K562	blood:	n/a	n/a
29	HCFC1	chr5:114960933-114962699	Hela-S3	cervix:	n/a	n/a
30	CHD1	chr5:114961109-114962517	GM12878	blood:	n/a	n/a
31	TBL1XR1	chr5:114961595-114962579	K562	blood:	n/a	n/a
32	MXI1	chr5:114960979-114962697	IMR90	lung:	n/a	n/a
33	TBP	chr5:114961589-114962619	Hela-S3	cervix:	n/a	n/a
34	MXI1	chr5:114960406-114962602	SK-N-SH	brain:	n/a	n/a
35	POLR2A	chr5:114961398-114962681	HEK293	kidney:	n/a	n/a
36	CREB1	chr5:114961160-114962517	HepG2	liver:	n/a	n/a
37	EGR1	chr5:114961371-114962533	HCT-116	colon:	n/a	chr5:114961887-114961900
38	CREB1	chr5:114961336-114962545	K562	blood:	n/a	n/a
39	MAX	chr5:114961155-114962475	HCT-116	colon:	n/a	n/a
40	SMARCC1	chr5:114961105-114962506	Hela-S3	cervix:	n/a	n/a
41	POLR2A	chr5:114961110-114962481	HepG2	liver:	n/a	n/a
42	POLR2A	chr5:114960905-114962578	PBDE	blood:	n/a	n/a
43	MTA3	chr5:114961177-114962480	GM12878	blood:	n/a	n/a
44	TBL1XR1	chr5:114961210-114962474	K562	blood:	n/a	n/a
45	POLR2A	chr5:114961431-114962506	HCT-116	colon:	n/a	n/a
46	CEBPB	chr5:114961594-114962489	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:114936247..114938177-chr5:114959534..114962655,3	K562	blood:
2	chr5:114960865..114962954-chr5:115170753..115172835,2	MCF-7	breast:
3	chr5:114960793..114963745-chr5:114966203..114968929,3	MCF-7	breast:
4	chr5:114961758..114963636-chr5:115175834..115179975,3	K562	blood:
5	chr5:114630838..114633826-chr5:114960976..114962823,3	MCF-7	breast:
6	chr5:114959789..114964126-chr5:115174280..115179155,11	MCF-7	breast:
7	chr5:114878501..114880649-chr5:114962329..114964863,2	K562	blood:
8	chr5:114630095..114632050-chr5:114960167..114962829,2	MCF-7	breast:
9	chr5:114960090..114964183-chr5:115419193..115421485,4	MCF-7	breast:
10	chr5:114959625..114963439-chr5:115175786..115178902,4	MCF-7	breast:
11	chr5:114961103..114964725-chr5:115175944..115179319,4	K562	blood:
12	chr5:114961228..114962989-chr5:115170828..115173503,2	MCF-7	breast:

Variant related genes	Relation type
TMED7-TICAM2	TF binding region
TICAM2	TF binding region
TMED7	TF binding region
ENSG00000145781	Chromatin interaction
ENSG00000164221	Chromatin interaction
ENSG00000243414	Chromatin interaction
ENSG00000249249	Chromatin interaction
ENSG00000177879	Chromatin interaction
ENSG00000145780	Chromatin interaction
ENSG00000145782	Chromatin interaction
ENSG00000134970	Chromatin interaction
ENSG00000271918	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs56774716	1.00[AFR][1000 genomes]
rs57651143	1.00[AFR][1000 genomes]
rs57806423	1.00[AFR][1000 genomes]
rs58527582	0.90[AFR][1000 genomes]
rs58575550	1.00[AFR][1000 genomes]
rs58727668	0.90[AFR][1000 genomes]
rs59498080	1.00[AFR][1000 genomes]
rs60230535	1.00[AFR][1000 genomes]
rs60326995	1.00[AFR][1000 genomes]
rs6873889	0.90[AFR][1000 genomes]
rs73254573	0.90[AFR][1000 genomes]
rs73254575	0.90[AFR][1000 genomes]
rs73254578	0.90[AFR][1000 genomes]
rs73254582	0.90[AFR][1000 genomes]
rs73254585	0.90[AFR][1000 genomes]
rs73254587	0.90[AFR][1000 genomes]
rs73254592	0.90[AFR][1000 genomes]
rs73254595	0.90[AFR][1000 genomes]
rs73254599	0.90[AFR][1000 genomes]
rs73254601	0.82[AFR][1000 genomes]
rs73256603	0.82[AFR][1000 genomes]
rs73260535	0.90[AFR][1000 genomes]
rs73260536	0.90[AFR][1000 genomes]
rs73260539	0.95[AFR][1000 genomes]
rs73260540	1.00[AFR][1000 genomes]
rs73260542	1.00[AFR][1000 genomes]
rs73260543	1.00[AFR][1000 genomes]
rs73260545	1.00[AFR][1000 genomes]
rs73260548	1.00[AFR][1000 genomes]
rs73260552	1.00[AFR][1000 genomes]
rs73260555	1.00[AFR][1000 genomes]
rs73260556	1.00[AFR][1000 genomes]
rs73260562	1.00[AFR][1000 genomes]
rs73260563	1.00[AFR][1000 genomes]
rs73260565	1.00[AFR][1000 genomes]
rs73260567	1.00[AFR][1000 genomes]
rs73260572	1.00[AFR][1000 genomes]
rs73260574	1.00[AFR][1000 genomes]
rs73260580	1.00[AFR][1000 genomes]
rs73260583	1.00[AFR][1000 genomes]
rs73260584	1.00[AFR][1000 genomes]
rs73260585	1.00[AFR][1000 genomes]
rs73260586	1.00[AFR][1000 genomes]
rs73264716	1.00[AFR][1000 genomes]
rs73264723	1.00[AFR][1000 genomes]
rs73264732	1.00[AFR][1000 genomes]
rs73264737	0.87[AFR][1000 genomes]
rs73264754	0.87[AFR][1000 genomes]
rs73264767	0.87[AFR][1000 genomes]
rs7341161	1.00[AFR][1000 genomes]
rs7722595	1.00[AFR][1000 genomes]
rs7722614	0.91[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916273	chr5:114656592-115089901	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv868915	chr5:114723371-115252527	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:114959600-114962600	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr5:114959600-114962800	Active TSS	GM12878-XiMat	blood
3	chr5:114960000-114962600	Active TSS	H9 Cell Line	embryonic stem cell
4	chr5:114960000-114962600	Active TSS	Breast Myoepithelial Primary Cells	Breast
5	chr5:114960000-114962600	Active TSS	Stomach Mucosa	stomach
6	chr5:114960200-114962600	Active TSS	H1 Cell Line	embryonic stem cell
7	chr5:114960200-114962600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr5:114960200-114962600	Active TSS	Fetal Muscle Trunk	muscle
9	chr5:114960200-114962600	Active TSS	HSMMtube	muscle
10	chr5:114960400-114962600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr5:114960400-114962600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr5:114960400-114962600	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr5:114960400-114962600	Active TSS	Placenta	Placenta
14	chr5:114960400-114962600	Active TSS	HSMM	muscle
15	chr5:114960400-114962600	Active TSS	K562	blood
16	chr5:114960600-114962600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr5:114960600-114962600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr5:114960600-114962600	Active TSS	Fetal Muscle Leg	muscle
19	chr5:114960600-114962600	Active TSS	Right Ventricle	heart
20	chr5:114960600-114962600	Active TSS	Stomach Smooth Muscle	stomach
21	chr5:114960600-114962600	Bivalent/Poised TSS	HepG2	liver
22	chr5:114960600-114962600	Active TSS	Osteobl	bone
23	chr5:114960800-114962600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
24	chr5:114960800-114962600	Active TSS	iPS-20b Cell Line	embryonic stem cell
25	chr5:114960800-114962600	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
26	chr5:114960800-114962600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
27	chr5:114960800-114962600	Active TSS	Colonic Mucosa	Colon
28	chr5:114961000-114962600	Active TSS	HUES48 Cell Line	embryonic stem cell
29	chr5:114961000-114962600	Active TSS	HUES64 Cell Line	embryonic stem cell
30	chr5:114961000-114962600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
31	chr5:114961000-114962600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr5:114961000-114962600	Active TSS	Colon Smooth Muscle	Colon
33	chr5:114961000-114962600	Active TSS	Duodenum Mucosa	Duodenum
34	chr5:114961000-114962600	Active TSS	Duodenum Smooth Muscle	Duodenum
35	chr5:114961000-114962600	Active TSS	Fetal Brain Male	brain
36	chr5:114961000-114962600	Active TSS	Fetal Brain Female	brain
37	chr5:114961000-114962600	Active TSS	Fetal Lung	lung
38	chr5:114961000-114962800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr5:114961200-114962600	Active TSS	iPS-18 Cell Line	embryonic stem cell
40	chr5:114961200-114962600	Active TSS	Primary monocytes fromperipheralblood	blood
41	chr5:114961200-114962600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
42	chr5:114961400-114963000	Active TSS	Thymus	Thymus
43	chr5:114961600-114962600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr5:114961800-114962600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr5:114962000-114962600	Flanking Active TSS	Primary hematopoietic stem cells	blood
46	chr5:114962200-114962600	Flanking Active TSS	Primary B cells from peripheral blood	blood
47	chr5:114962200-114962600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
48	chr5:114962200-114962600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
49	chr5:114962200-114962600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
50	chr5:114962200-114962600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--

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