Variant report

Variant	rs72827885
Chromosome Location	chr17:46534423-46534424
allele	C/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	MAX	chr17:46533636-46535189	HCT-116	colon:	n/a	chr17:46534108-46534119 chr17:46534110-46534119 chr17:46534109-46534118 chr17:46534108-46534119 chr17:46534850-46534860 chr17:46534109-46534118 chr17:46534109-46534118 chr17:46534107-46534120
2	SMC3	chr17:46534361-46535285	SK-N-SH	brain:	n/a	n/a
3	MAX	chr17:46533788-46535178	HCT-116	colon:	n/a	chr17:46534108-46534119 chr17:46534110-46534119 chr17:46534109-46534118 chr17:46534108-46534119 chr17:46534850-46534860 chr17:46534109-46534118 chr17:46534109-46534118 chr17:46534107-46534120
4	CTCF	chr17:46534283-46535073	MCF-7	breast:	n/a	chr17:46534792-46534808 chr17:46534791-46534809 chr17:46534793-46534806
5	CEBPB	chr17:46534345-46535013	MCF-7	breast:	n/a	n/a
6	MAX	chr17:46534396-46535104	MCF-7	breast:	n/a	chr17:46534850-46534860
7	ZEB1	chr17:46534324-46534931	GM12878	blood:	n/a	n/a
8	CTCF	chr17:46534254-46535134	HCT-116	colon:	n/a	chr17:46534792-46534808 chr17:46534791-46534809 chr17:46534793-46534806
9	TCF12	chr17:46534399-46534576	H1-hESC	embryonic stem cell:	n/a	n/a
10	CTCF	chr17:46534208-46535512	SK-N-SH	brain:	n/a	chr17:46534792-46534808 chr17:46534791-46534809 chr17:46534793-46534806
11	MAX	chr17:46534412-46535130	A549	lung:	n/a	chr17:46534850-46534860
12	RAD21	chr17:46534422-46535191	SK-N-SH	brain:	n/a	chr17:46534789-46534808
13	TEAD4	chr17:46534095-46534451	H1-hESC	embryonic stem cell:	n/a	n/a
14	TCF3	chr17:46534418-46534930	GM12878	blood:	n/a	n/a
15	TCF12	chr17:46534373-46535079	A549	lung:	n/a	n/a
16	CTCF	chr17:46534337-46535060	MCF-7	breast:	n/a	chr17:46534792-46534808 chr17:46534791-46534809 chr17:46534793-46534806
17	CTCF	chr17:46534032-46535649	A549	lung:	n/a	chr17:46534792-46534808 chr17:46534791-46534809 chr17:46534793-46534806
18	KAP1	chr17:46533972-46535073	HEK293	kidney:	n/a	n/a
19	CTCF	chr17:46534062-46535196	HCT-116	colon:	n/a	chr17:46534792-46534808 chr17:46534791-46534809 chr17:46534793-46534806
20	RAD21	chr17:46533842-46535224	HCT-116	colon:	n/a	chr17:46534789-46534808
21	USF1	chr17:46533583-46535060	HCT-116	colon:	n/a	chr17:46534107-46534118
22	TCF12	chr17:46534418-46534933	GM12878	blood:	n/a	n/a
23	SIN3A	chr17:46533951-46534931	H1-hESC	embryonic stem cell:	n/a	chr17:46534108-46534117
24	E2F6	chr17:46534397-46535058	H1-hESC	embryonic stem cell:	n/a	n/a
25	MAZ	chr17:46534279-46535321	IMR90	lung:	n/a	chr17:46534850-46534860
26	USF1	chr17:46533736-46535068	HCT-116	colon:	n/a	chr17:46534107-46534118
27	MAX	chr17:46534391-46535052	MCF-7	breast:	n/a	chr17:46534850-46534860
28	CREB1	chr17:46534371-46534926	A549	lung:	n/a	n/a
29	KAP1	chr17:46533898-46534992	U2OS	brain:	n/a	n/a
30	ZEB1	chr17:46534405-46534694	GM12878	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr17:46534400-46534450	SK-N-SH_RA	brain:	n/a
2	chr17:46534400-46534450	LNCaP	prostate:	n/a
3	chr17:46534400-46534450	PANC-1	pancreas:	n/a
4	chr17:46534400-46534450	BJ	skin:	n/a
5	chr17:46534400-46534450	MCF10A-Er-Src	breast:	n/a
6	chr17:46534400-46534450	AG09309	skin:	n/a
7	chr17:46534400-46534450	HCPEpiC	choroid plexus:	n/a
8	chr17:46534400-46534450	Jurkat	blood:	n/a
9	chr17:46534400-46534450	Hepatocyte	liver:	n/a
10	chr17:46534400-46534450	AG04449	skin:	fetal
11	chr17:46534400-46534450	GM12892	blood:	n/a
12	chr17:46534400-46534450	AG04450	lung:	fetal
13	chr17:46534400-46534450	HCM	heart:	n/a
14	chr17:46534400-46534450	HL-60	blood:	n/a
15	chr17:46534400-46534450	A549	lung:	n/a
16	chr17:46534400-46534450	HRPEpiC	eye:	n/a
17	chr17:46534400-46534450	NHDF-neo	bronchial:	n/a
18	chr17:46534400-46534450	GM12891	blood:	n/a
19	chr17:46534400-46534450	HMEC	breast:	n/a
20	chr17:46534400-46534450	HAEpiC	amniotic membrane:	n/a
21	chr17:46534400-46534450	GM19239	blood:	n/a
22	chr17:46534400-46534450	NT2-D1	testis:	n/a
23	chr17:46534400-46534450	AoSMC	blood vessel:	n/a
24	chr17:46534400-46534450	HIPEpiC	eye:	n/a
25	chr17:46534400-46534450	AG10803	skin:	n/a
26	chr17:46534400-46534450	GM06990	blood:	n/a
27	chr17:46534400-46534450	HPAEpiC	pulmonary alveolar:	n/a
28	chr17:46534400-46534450	PFSK-1	brain:	n/a
29	chr17:46534400-46534450	CMK	blood:	n/a
30	chr17:46534400-46534450	BE2_C	brain:	n/a
31	chr17:46534400-46534450	AG09319	gingival:	n/a
32	chr17:46534400-46534450	NB4	blood:	n/a
33	chr17:46534400-46534450	SK-N-SH	brain:	n/a
34	chr17:46534400-46534450	U87	brain:	n/a
35	chr17:46534400-46534450	ovcar-3	ovarian:	n/a
36	chr17:46534400-46534450	HEK293	kidney:	embryo
37	chr17:46534400-46534450	Caco-2	colon:	n/a
38	chr17:46534400-46534450	HCF	heart:	n/a
39	chr17:46534400-46534450	Hela-S3	cervix:	n/a
40	chr17:46534400-46534450	HEEpiC	esophagus:	n/a
41	chr17:46534400-46534450	RPTEC	kidney:	n/a
42	chr17:46534400-46534450	HNPCEpiC	eye:	n/a
43	chr17:46534400-46534450	HCT-116	colon:	n/a
44	chr17:46534400-46534450	T-47D	breast:	n/a
45	chr17:46534400-46534450	IMR90	lung:	fetal
46	chr17:46534400-46534450	SK-N-MC	brain:	n/a
47	chr17:46534400-46534450	HRE	kidney:	n/a
48	chr17:46534400-46534450	NH-A	brain:	n/a
49	chr17:46534400-46534450	GM12878	blood:	n/a
50	chr17:46534400-46534450	H1-hESC	embryonic stem cell:	embryo

No.	Distal block	Cell Line	Cell type
1	chr17:46451741..46452424-chr17:46534380..46535095,2	MCF-7	breast:
2	chr17:46412890..46413642-chr17:46534395..46535175,2	MCF-7	breast:
3	chr17:46516365..46518843-chr17:46533348..46535328,2	K562	blood:
4	chr17:46534303..46534843-chr17:46670959..46671869,2	K562	blood:
5	chr17:46533875..46534810-chr20:55548699..55549682,2	MCF-7	breast:
6	chr17:46523948..46525611-chr17:46533793..46535794,2	K562	blood:
7	chr17:46534407..46535828-chr17:46695754..46696608,3	K562	blood:
8	chr17:46230746..46231690-chr17:46534208..46535239,3	MCF-7	breast:
9	chr17:46529747..46531538-chr17:46533200..46534780,2	K562	blood:
10	chr17:46532737..46535111-chr17:46677941..46680284,2	K562	blood:
11	chr17:46532772..46535087-chr17:46626346..46628551,2	K562	blood:

Variant related genes	Relation type
ENSG00000264451	TF binding region
ENSG00000264451	CpG island
ENSG00000233101	Chromatin interaction
ENSG00000120075	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1472966	0.85[EUR][1000 genomes]
rs17624626	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17695373	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17696392	0.85[EUR][1000 genomes]
rs72827814	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72827830	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72827832	0.85[EUR][1000 genomes]
rs72827834	0.85[EUR][1000 genomes]
rs72827876	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72827877	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72827882	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72827887	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72827899	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs72827901	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][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	nsv833469	chr17:46491849-46709406	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	349 gene(s)	inside rSNPs	diseases
2	esv3420538	chr17:46504944-46861553	Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	369 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46528800-46535200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
2	chr17:46529000-46535400	Enhancers	Fetal Thymus	thymus
3	chr17:46532000-46535200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
4	chr17:46533600-46535000	Enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr17:46533800-46534600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr17:46533800-46534600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
7	chr17:46533800-46534600	Bivalent Enhancer	Fetal Intestine Small	intestine
8	chr17:46533800-46534800	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr17:46533800-46534800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr17:46533800-46534800	Bivalent Enhancer	Duodenum Mucosa	Duodenum
11	chr17:46533800-46535200	Enhancers	Primary B cells from peripheral blood	blood
12	chr17:46534000-46534600	Flanking Bivalent TSS/Enh	ES-I3 Cell Line	embryonic stem cell
13	chr17:46534000-46534600	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
14	chr17:46534000-46534600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr17:46534000-46534600	Enhancers	Placenta Amnion	Placenta Amnion
16	chr17:46534000-46534600	Enhancers	Sigmoid Colon	Sigmoid Colon
17	chr17:46534000-46534800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr17:46534000-46534800	Enhancers	Esophagus	oesophagus
19	chr17:46534000-46535200	Enhancers	HMEC	breast
20	chr17:46534200-46534600	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
21	chr17:46534200-46534600	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
22	chr17:46534200-46534600	Bivalent Enhancer	Stomach Mucosa	stomach
23	chr17:46534200-46534800	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
24	chr17:46534200-46534800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
25	chr17:46534200-46534800	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
26	chr17:46534200-46534800	Flanking Active TSS	Primary T cells from cord blood	blood
27	chr17:46534200-46534800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
28	chr17:46534200-46534800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
29	chr17:46534200-46534800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
30	chr17:46534200-46534800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
31	chr17:46534200-46534800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
32	chr17:46534200-46535000	Bivalent Enhancer	Liver	Liver
33	chr17:46534200-46535000	Enhancers	Thymus	Thymus
34	chr17:46534200-46535000	Flanking Active TSS	GM12878-XiMat	blood
35	chr17:46534200-46535200	Enhancers	Primary B cells from cord blood	blood
36	chr17:46534400-46534600	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
37	chr17:46534400-46534600	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr17:46534400-46534600	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr17:46534400-46534600	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr17:46534400-46534600	Enhancers	Adipose Nuclei	Adipose
41	chr17:46534400-46534600	Bivalent Enhancer	Brain Angular Gyrus	brain
42	chr17:46534400-46534600	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
43	chr17:46534400-46534600	Bivalent/Poised TSS	Fetal Kidney	kidney
44	chr17:46534400-46534600	Bivalent Enhancer	Lung	lung
45	chr17:46534400-46534600	Active TSS	Rectal Smooth Muscle	rectum
46	chr17:46534400-46534600	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle
47	chr17:46534400-46534800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr17:46534400-46534800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr17:46534400-46534800	Flanking Bivalent TSS/Enh	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr17:46534400-46534800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links