Variant report

Variant	rs4338843
Chromosome Location	chr17:20799723-20799724
allele	A/G
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	chr17:20798809-20800181	H1-hESC	embryonic stem cell:	n/a	n/a
2	CTCF	chr17:20799600-20799750	GM12869	blood:	n/a	chr17:20799603-20799621
3	CTCF	chr17:20799448-20799762	K562	blood:	n/a	chr17:20799603-20799621
4	CTCF	chr17:20799208-20799935	A549	lung:	n/a	chr17:20799603-20799621
5	CTCF	chr17:20799530-20799743	GM12878	blood:	n/a	chr17:20799603-20799621
6	CTCF	chr17:20799475-20799774	MCF-7	breast:	n/a	chr17:20799603-20799621
7	CTCF	chr17:20799263-20799833	A549	lung:	n/a	chr17:20799603-20799621
8	TCF12	chr17:20799564-20799765	GM12878	blood:	n/a	n/a
9	CTCF	chr17:20799600-20799750	HFF-Myc	foreskin:	n/a	chr17:20799603-20799621
10	POLR2A	chr17:20799288-20799983	H1-hESC	embryonic stem cell:	n/a	n/a
11	CTCF	chr17:20799565-20799762	GM12891	blood:	n/a	chr17:20799603-20799621
12	CTCF	chr17:20799486-20799752	MCF-7	breast:	n/a	chr17:20799603-20799621
13	CTCF	chr17:20799580-20799730	HAc	cerebellar:	n/a	chr17:20799603-20799621
14	CTCF	chr17:20799485-20799725	MCF-7	breast:	n/a	chr17:20799603-20799621
15	RAD21	chr17:20799397-20799737	H1-hESC	embryonic stem cell:	n/a	chr17:20799604-20799623
16	PAX5	chr17:20799256-20799747	GM12878	blood:	n/a	chr17:20799510-20799529 chr17:20799511-20799528
17	CTCF	chr17:20799476-20799777	MCF-7	breast:	n/a	chr17:20799603-20799621
18	RAD21	chr17:20799485-20799724	IMR90	lung:	n/a	chr17:20799604-20799623
19	PAX5	chr17:20799230-20799786	GM12878	blood:	n/a	chr17:20799510-20799529 chr17:20799511-20799528
20	CTCF	chr17:20799450-20799848	K562	blood:	n/a	chr17:20799603-20799621
21	CTCF	chr17:20799467-20799738	Gliobla	brain:	n/a	chr17:20799603-20799621
22	MYC	chr17:20799621-20799804	MCF-7	breast:	n/a	n/a
23	POLR2A	chr17:20799540-20799745	HepG2	liver:	n/a	n/a
24	CTCF	chr17:20799359-20799756	A549	lung:	n/a	chr17:20799603-20799621
25	POLR2A	chr17:20799279-20799899	H1-hESC	embryonic stem cell:	n/a	n/a
26	CTCF	chr17:20799354-20799949	K562	blood:	n/a	chr17:20799603-20799621
27	POLR2A	chr17:20799369-20799780	K562	blood:	n/a	n/a
28	CTCF	chr17:20799379-20799756	A549	lung:	n/a	chr17:20799603-20799621
29	POLR2A	chr17:20798830-20799886	H1-hESC	embryonic stem cell:	n/a	n/a
30	CTCF	chr17:20799664-20799774	GM19238	blood:	n/a	n/a
31	CTCF	chr17:20799475-20799771	MCF-7	breast:	n/a	chr17:20799603-20799621
32	CTCF	chr17:20799600-20799750	HCM	heart:	n/a	chr17:20799603-20799621
33	EBF1	chr17:20799559-20799878	GM12878	blood:	n/a	n/a
34	CTCF	chr17:20799488-20799758	A549	lung:	n/a	chr17:20799603-20799621

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr17:20799676-20799726	NH-A	brain:	n/a
2	chr17:20799676-20799726	SKMC	muscle:	n/a
3	chr17:20799676-20799726	MCF-7	breast:	n/a
4	chr17:20799714-20799764	NHBE	bronchial:	n/a
5	chr17:20799714-20799764	LNCaP	prostate:	n/a
6	chr17:20799676-20799726	AG04450	lung:	fetal
7	chr17:20799676-20799726	HIPEpiC	eye:	n/a
8	chr17:20799714-20799764	GM19239	blood:	n/a
9	chr17:20799714-20799764	HCT-116	colon:	n/a
10	chr17:20799714-20799764	CMK	blood:	n/a
11	chr17:20799714-20799764	H1-hESC	embryonic stem cell:	embryo
12	chr17:20799714-20799764	HNPCEpiC	eye:	n/a
13	chr17:20799676-20799726	HMEC	breast:	n/a
14	chr17:20799676-20799726	Caco-2	colon:	n/a
15	chr17:20799676-20799726	HNPCEpiC	eye:	n/a
16	chr17:20799676-20799726	A549	lung:	n/a
17	chr17:20799714-20799764	HRE	kidney:	n/a
18	chr17:20799714-20799764	PrEC	prostate:	n/a
19	chr17:20799676-20799726	ovcar-3	ovarian:	n/a
20	chr17:20799676-20799726	BJ	skin:	n/a
21	chr17:20799676-20799726	U87	brain:	n/a
22	chr17:20799714-20799764	AG10803	skin:	n/a
23	chr17:20799714-20799764	ovcar-3	ovarian:	n/a
24	chr17:20799676-20799726	NT2-D1	testis:	n/a
25	chr17:20799676-20799726	ProgFib	skin:	n/a
26	chr17:20799676-20799726	PANC-1	pancreas:	n/a
27	chr17:20799714-20799764	SK-N-SH_RA	brain:	n/a
28	chr17:20799714-20799764	ProgFib	skin:	n/a
29	chr17:20799714-20799764	AG04450	lung:	fetal
30	chr17:20799676-20799726	NHDF-neo	bronchial:	n/a
31	chr17:20799714-20799764	U87	brain:	n/a
32	chr17:20799676-20799726	SK-N-MC	brain:	n/a
33	chr17:20799714-20799764	A549	lung:	n/a
34	chr17:20799676-20799726	SK-N-SH	brain:	n/a
35	chr17:20799676-20799726	AG04449	skin:	fetal
36	chr17:20799714-20799764	NH-A	brain:	n/a
37	chr17:20799676-20799726	HEEpiC	esophagus:	n/a
38	chr17:20799676-20799726	HCM	heart:	n/a
39	chr17:20799676-20799726	NHBE	bronchial:	n/a
40	chr17:20799676-20799726	HRPEpiC	eye:	n/a
41	chr17:20799714-20799764	BE2_C	brain:	n/a
42	chr17:20799676-20799726	HRE	kidney:	n/a
43	chr17:20799714-20799764	HL-60	blood:	n/a
44	chr17:20799714-20799764	HEK293	kidney:	embryo
45	chr17:20799714-20799764	PANC-1	pancreas:	n/a
46	chr17:20799714-20799764	HRPEpiC	eye:	n/a
47	chr17:20799676-20799726	Hepatocyte	liver:	n/a
48	chr17:20799676-20799726	GM12891	blood:	n/a
49	chr17:20799714-20799764	SAEC	small airway:	n/a
50	chr17:20799714-20799764	GM06990	blood:	n/a

Variant related genes	Relation type
RNU6-1178P	TF binding region
CCDC144NL	TF binding region
CCDC144NL	CpG island
RNU6-1178P	CpG island

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11204322	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11654155	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11657425	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11869464	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11870741	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11870757	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12451605	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12453688	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17841430	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17841431	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4132938	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57960567	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59791483	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7502207	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7502919	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9890010	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9902704	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][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	nsv916440	chr17:20171468-20839266	ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	esv2751619	chr17:20462908-20914156	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	esv3361931	chr17:20539962-20845258	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	esv3330516	chr17:20572433-20862663	Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv960439	chr17:20733458-20799926	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:20780800-20801600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr17:20782600-20801200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr17:20789400-20801800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr17:20798200-20801200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr17:20798200-20811600	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr17:20798600-20801200	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr17:20798800-20800200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr17:20798800-20806800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr17:20799000-20799800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr17:20799000-20800000	Strong transcription	H1 Cell Line	embryonic stem cell
11	chr17:20799200-20799800	Genic enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr17:20799200-20800000	Active TSS	Fetal Brain Female	brain
13	chr17:20799200-20800200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr17:20799400-20799800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr17:20799400-20799800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr17:20799400-20799800	Enhancers	Gastric	stomach
17	chr17:20799400-20800000	Active TSS	Muscle Satellite Cultured Cells	--
18	chr17:20799600-20799800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
19	chr17:20799600-20799800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr17:20799600-20799800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr17:20799600-20799800	Bivalent Enhancer	Adipose Nuclei	Adipose
22	chr17:20799600-20799800	Bivalent/Poised TSS	Colonic Mucosa	Colon
23	chr17:20799600-20800000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr17:20799600-20800000	Active TSS	Pancreas	Pancrea
25	chr17:20799600-20800200	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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