Variant report

Variant	rs17839551
Chromosome Location	chr16:30363382-30363383
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:59)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:59 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFIC	chr16:30362891-30364020	ECC-1	luminal epithelium:	n/a	n/a
2	FOS	chr16:30363368-30363793	MCF10A-Er-Src	breast:	n/a	chr16:30363586-30363597
3	NFIC	chr16:30363044-30364029	SK-N-SH	brain:	n/a	n/a
4	PBX3	chr16:30363375-30363876	SK-N-SH	brain:	n/a	n/a
5	MAX	chr16:30363369-30363840	SK-N-SH	brain:	n/a	n/a
6	ZBTB7A	chr16:30363140-30363774	ECC-1	luminal epithelium:	n/a	n/a
7	MBD4	chr16:30363289-30364855	HepG2	liver:	n/a	n/a
8	POLR2A	chr16:30363137-30363914	U87	brain:	n/a	n/a
9	POLR2A	chr16:30362407-30364951	HepG2	liver:	n/a	n/a
10	POLR2A	chr16:30363133-30364007	K562	blood:	n/a	n/a
11	MAX	chr16:30363369-30363919	A549	lung:	n/a	n/a
12	FOSL2	chr16:30362903-30364923	HepG2	liver:	n/a	n/a
13	TCF12	chr16:30363024-30363957	ECC-1	luminal epithelium:	n/a	n/a
14	FOSL2	chr16:30363295-30363938	SK-N-SH	brain:	n/a	n/a
15	POLR2A	chr16:30363231-30363886	HUVEC	blood vessel:	n/a	n/a
16	MAZ	chr16:30363159-30363720	IMR90	lung:	n/a	n/a
17	MYBL2	chr16:30363346-30363841	HepG2	liver:	n/a	n/a
18	TCF7L2	chr16:30363368-30363773	Hela-S3	cervix:	n/a	n/a
19	CEBPD	chr16:30363366-30363748	HepG2	liver:	n/a	n/a
20	POLR2A	chr16:30363340-30363791	U87	brain:	n/a	n/a
21	POLR2A	chr16:30363228-30364132	K562	blood:	n/a	n/a
22	POLR2A	chr16:30360110-30369693	HepG2	liver:	n/a	n/a
23	POLR2A	chr16:30363271-30363748	HUVEC	blood vessel:	n/a	n/a
24	STAT3	chr16:30363279-30363718	MCF10A-Er-Src	breast:	n/a	n/a
25	JUND	chr16:30363266-30363957	SK-N-SH	brain:	n/a	n/a
26	POLR2A	chr16:30362921-30363829	PANC-1	pancreas:	n/a	n/a
27	TEAD4	chr16:30363228-30363785	ECC-1	luminal epithelium:	n/a	n/a
28	POLR2A	chr16:30363215-30363770	ECC-1	luminal epithelium:	n/a	n/a
29	SIN3AK20	chr16:30363345-30363804	SK-N-SH	brain:	n/a	n/a
30	TEAD4	chr16:30363124-30363897	ECC-1	luminal epithelium:	n/a	n/a
31	POLR2A	chr16:30363269-30365340	HepG2	liver:	n/a	n/a
32	POLR2A	chr16:30363361-30364025	PANC-1	pancreas:	n/a	n/a
33	EP300	chr16:30362937-30363948	ECC-1	luminal epithelium:	n/a	n/a
34	POLR2A	chr16:30362863-30364114	K562	blood:	n/a	n/a
35	FOS	chr16:30363353-30363769	MCF10A-Er-Src	breast:	n/a	chr16:30363586-30363597
36	POLR2A	chr16:30363301-30363788	HUVEC	blood vessel:	n/a	n/a
37	POLR2A	chr16:30361391-30369063	HepG2	liver:	n/a	n/a
38	POLR2A	chr16:30362848-30364698	HepG2	liver:	n/a	n/a
39	MYC	chr16:30363382-30363770	MCF10A-Er-Src	breast:	n/a	n/a
40	POLR2A	chr16:30363340-30363764	HCT-116	colon:	n/a	n/a
41	POLR2A	chr16:30363085-30363914	U87	brain:	n/a	n/a
42	FOXM1	chr16:30363019-30363945	ECC-1	luminal epithelium:	n/a	n/a
43	STAT3	chr16:30363290-30363706	MCF10A-Er-Src	breast:	n/a	n/a
44	HEY1	chr16:30362666-30363472	HepG2	liver:	n/a	n/a
45	FOSL2	chr16:30363296-30363895	A549	lung:	n/a	n/a
46	EP300	chr16:30363132-30363794	ECC-1	luminal epithelium:	n/a	n/a
47	TCF12	chr16:30363036-30363943	ECC-1	luminal epithelium:	n/a	n/a
48	POLR2A	chr16:30363265-30363874	SK-N-SH	brain:	n/a	n/a
49	NFIC	chr16:30363033-30363999	ECC-1	luminal epithelium:	n/a	n/a
50	MAX	chr16:30363182-30363865	ECC-1	luminal epithelium:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:30352836..30354996-chr16:30361711..30364215,3	MCF-7	breast:
2	chr16:30362931..30364603-chr16:30670116..30672156,2	MCF-7	breast:
3	chr16:30352018..30354581-chr16:30361515..30364164,2	K562	blood:
4	chr16:30362121..30363663-chr16:30386245..30389219,2	K562	blood:
5	chr16:30347434..30350400-chr16:30361325..30364299,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000260219	TF binding region
ENSG00000180209	Chromatin interaction
ENSG00000156860	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs3766	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4076091	0.86[AMR][1000 genomes]
rs4788412	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56353063	0.98[AMR][1000 genomes];0.96[EUR][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	nsv1061165	chr16:29657389-30363743	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	245 gene(s)	inside rSNPs	diseases
2	nsv1065915	chr16:29967090-30486120	Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	229 gene(s)	inside rSNPs	diseases
3	nsv542897	chr16:29967090-30486120	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	229 gene(s)	inside rSNPs	diseases
4	esv2758420	chr16:30073955-30383280	Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	140 gene(s)	inside rSNPs	diseases
5	esv2758642	chr16:30073955-30383280	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	140 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17839551	ZNF768	cis	parietal	SCAN
rs17839551	BCL7C	cis	cerebellum	SCAN
rs17839551	YPEL3	cis	Esophagus Muscularis	GTEx
rs17839551	CCDC101	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:30347400-30363400	Weak transcription	Brain Angular Gyrus	brain
2	chr16:30360000-30363800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr16:30360200-30365600	Weak transcription	Fetal Kidney	kidney
4	chr16:30360400-30365000	Strong transcription	Primary T helper cells PMA-I stimulated	--
5	chr16:30360600-30363400	Strong transcription	Fetal Stomach	stomach
6	chr16:30360600-30364000	Strong transcription	Primary T helper cells fromperipheralblood	blood
7	chr16:30360600-30364600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr16:30360600-30365200	Strong transcription	Sigmoid Colon	Sigmoid Colon
9	chr16:30360600-30365200	Strong transcription	NHEK	skin
10	chr16:30360800-30365000	Strong transcription	Fetal Thymus	thymus
11	chr16:30360800-30365200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr16:30361000-30363400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr16:30361000-30363400	Strong transcription	Dnd41	blood
14	chr16:30361000-30363400	Strong transcription	HMEC	breast
15	chr16:30361000-30364400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr16:30361000-30364400	Strong transcription	Placenta	Placenta
17	chr16:30361000-30364600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr16:30361000-30364600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr16:30361000-30364600	Strong transcription	K562	blood
20	chr16:30361000-30365200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr16:30361000-30365200	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr16:30361000-30365200	Strong transcription	Primary neutrophils fromperipheralblood	blood
23	chr16:30361000-30365400	Strong transcription	Primary T cells from cord blood	blood
24	chr16:30361000-30365400	Genic enhancers	Fetal Intestine Small	intestine
25	chr16:30361000-30365400	Strong transcription	Thymus	Thymus
26	chr16:30361200-30364800	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr16:30361200-30365000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr16:30361200-30365200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr16:30361200-30365400	Strong transcription	HUES6 Cell Line	embryonic stem cell
30	chr16:30361400-30364400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr16:30361400-30365200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr16:30361400-30365200	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr16:30361600-30364800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
34	chr16:30361600-30364800	Strong transcription	Primary T killer memory cells from peripheral blood	blood
35	chr16:30361600-30365000	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr16:30361600-30365000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr16:30361600-30365000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr16:30361600-30365000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr16:30361600-30365200	Strong transcription	H1 Cell Line	embryonic stem cell
40	chr16:30361600-30365200	Strong transcription	Rectal Mucosa Donor 31	rectum
41	chr16:30361600-30365400	Strong transcription	H9 Cell Line	embryonic stem cell
42	chr16:30361600-30365400	Strong transcription	HUES48 Cell Line	embryonic stem cell
43	chr16:30361600-30365400	Strong transcription	HUES64 Cell Line	embryonic stem cell
44	chr16:30361600-30365400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
45	chr16:30361600-30365400	Genic enhancers	Duodenum Mucosa	Duodenum
46	chr16:30361600-30365600	Genic enhancers	Primary T cells fromperipheralblood	blood
47	chr16:30361600-30366000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
48	chr16:30361800-30364200	Genic enhancers	NH-A	brain
49	chr16:30361800-30364400	Genic enhancers	HUVEC	blood vessel
50	chr16:30361800-30364800	Genic enhancers	Liver	Liver

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