Variant report

Variant	rs16860620
Chromosome Location	chr4:47706889-47706890
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:211)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:211 , 50 per page) page: 1 2 3 4 5

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr4:47706800-47706950	GM12875	blood:	n/a	n/a
2	RAD21	chr4:47706618-47707203	HCT-116	colon:	n/a	n/a
3	CTCF	chr4:47706813-47707050	MCF-7	breast:	n/a	n/a
4	SMC3	chr4:47706508-47708328	SK-N-SH	brain:	n/a	chr4:47707799-47707813
5	CTCF	chr4:47706840-47706990	GM12870	blood:	n/a	n/a
6	CTCF	chr4:47706812-47706992	Lung_OC	lung:	n/a	n/a
7	CTCF	chr4:47706760-47706910	HCT-116	colon:	n/a	n/a
8	CTCF	chr4:47706670-47707306	SK-N-SH	brain:	n/a	n/a
9	CTCF	chr4:47706784-47707050	MCF-7	breast:	n/a	n/a
10	CTCF	chr4:47706703-47707103	A549	lung:	n/a	n/a
11	CTCF	chr4:47706860-47707010	GM12867	blood:	n/a	n/a
12	CTCF	chr4:47706715-47707126	T-47D	breast:	n/a	n/a
13	CTCF	chr4:47706788-47707052	ProgFib	skin:	n/a	n/a
14	MYC	chr4:47706868-47706958	HUVEC	blood vessel:	n/a	n/a
15	CTCF	chr4:47706840-47706990	HEEpiC	esophagus:	n/a	n/a
16	CTCF	chr4:47706840-47706990	HBMEC	blood vessel:	n/a	n/a
17	CTCF	chr4:47706720-47707080	T-47D	breast:	n/a	n/a
18	RAD21	chr4:47706744-47707149	IMR90	lung:	n/a	n/a
19	CTCF	chr4:47706840-47706990	HCFaa	heart:	n/a	n/a
20	CTCF	chr4:47706880-47707030	GM12873	blood:	n/a	n/a
21	CTCF	chr4:47706644-47707117	IMR90	lung:	n/a	n/a
22	CTCF	chr4:47706783-47707039	LNCaP	prostate:	n/a	n/a
23	CTCF	chr4:47706792-47707054	NHEK	skin:	n/a	n/a
24	CTCF	chr4:47706860-47707010	HPF	lung:	n/a	n/a
25	CTCF	chr4:47706800-47706950	Hela-S3	cervix:	n/a	n/a
26	CTCF	chr4:47706799-47707056	A549	lung:	n/a	n/a
27	MAX	chr4:47706744-47707103	H1-hESC	embryonic stem cell:	n/a	n/a
28	CTCF	chr4:47706845-47707005	Spleen_OC	spleen:	n/a	n/a
29	CTCF	chr4:47706800-47706950	GM12868	blood:	n/a	n/a
30	CTCF	chr4:47706800-47706950	GM12872	blood:	n/a	n/a
31	CTCF	chr4:47706798-47707047	LNCaP	prostate:	n/a	n/a
32	CTCF	chr4:47706733-47707073	K562	blood:	n/a	n/a
33	MAX	chr4:47706682-47707094	K562	blood:	n/a	n/a
34	RAD21	chr4:47706646-47707138	MCF-7	breast:	n/a	n/a
35	MAX	chr4:47706668-47707073	MCF-7	breast:	n/a	n/a
36	CTCF	chr4:47706760-47706910	HFF	foreskin:	n/a	n/a
37	CTCF	chr4:47706820-47706970	Caco-2	colon:	n/a	n/a
38	CTCF	chr4:47706780-47706930	GM12864	blood:	n/a	n/a
39	CTCF	chr4:47706816-47707032	GM13977	blood:	n/a	n/a
40	CTCF	chr4:47706860-47707010	Hela-S3	cervix:	n/a	n/a
41	CTCF	chr4:47706818-47707040	H1-hESC	embryonic stem cell:	n/a	n/a
42	CTCF	chr4:47706800-47706950	HMEC	breast:	n/a	n/a
43	ZNF143	chr4:47706771-47707029	GM12878	blood:	n/a	n/a
44	MAX	chr4:47706654-47707071	MCF-7	breast:	n/a	n/a
45	CTCF	chr4:47706840-47706990	AG10803	skin:	n/a	n/a
46	CTCF	chr4:47706760-47706910	HVMF	connective:	n/a	n/a
47	CTCF	chr4:47706751-47707075	Gliobla	brain:	n/a	n/a
48	CTCF	chr4:47706800-47706950	HCM	heart:	n/a	n/a
49	SMC3	chr4:47706734-47707305	Hela-S3	cervix:	n/a	n/a
50	CTCF	chr4:47706821-47707012	GM10266	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:47706458..47708260-chr4:47841005..47842113,10	MCF-7	breast:
2	chr4:47706419..47708274-chr4:47838366..47839313,9	MCF-7	breast:
3	chr4:47706836..47707551-chr4:47840198..47840747,2	MCF-7	breast:
4	chr4:47670607..47671485-chr4:47706644..47707642,3	MCF-7	breast:
5	chr4:47706456..47708112-chr4:47838146..47839411,13	MCF-7	breast:
6	chr4:47706404..47706962-chr4:48089093..48089631,2	MCF-7	breast:
7	chr4:47706546..47707227-chr4:48088499..48089380,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000242262	TF binding region

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11723646	1.00[YRI][hapmap]
rs16860610	1.00[YRI][hapmap]
rs16860615	1.00[AMR][1000 genomes]
rs16860617	1.00[AMR][1000 genomes]
rs16860618	1.00[AMR][1000 genomes]
rs61761817	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008515	chr4:47488431-47906835	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv948568	chr4:47488431-47907524	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv1004939	chr4:47488573-47901460	Bivalent Enhancer Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv537080	chr4:47488573-47901460	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv997471	chr4:47489412-47895223	Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv998892	chr4:47493552-47863354	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
7	nsv537081	chr4:47493552-47863354	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
8	nsv1000337	chr4:47493907-47902019	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
9	nsv594118	chr4:47560386-47917730	Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
10	nsv829924	chr4:47670905-47866665	Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv879007	chr4:47688064-47752554	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:47646400-47707400	Weak transcription	Right Ventricle	heart
2	chr4:47704400-47709600	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr4:47705200-47707800	Enhancers	Fetal Lung	lung
4	chr4:47705400-47707000	Enhancers	Fetal Heart	heart
5	chr4:47706200-47707200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr4:47706200-47707600	Bivalent Enhancer	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr4:47706200-47707600	Flanking Active TSS	Liver	Liver
8	chr4:47706600-47707200	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr4:47706600-47707200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr4:47706600-47707200	Enhancers	Psoas Muscle	Psoas
11	chr4:47706600-47707400	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr4:47706600-47708200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr4:47706800-47707000	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr4:47706800-47707000	Enhancers	Placenta	Placenta
15	chr4:47706800-47707000	Enhancers	Left Ventricle	heart
16	chr4:47706800-47707200	Enhancers	Primary neutrophils fromperipheralblood	blood
17	chr4:47706800-47707200	Flanking Active TSS	Fetal Kidney	kidney
18	chr4:47706800-47707600	Flanking Active TSS	HepG2	liver
19	chr4:47706800-47707800	Enhancers	Adipose Nuclei	Adipose

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