Variant report

Variant	rs16860770
Chromosome Location	chr3:112994712-112994713
allele	G/T
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	CTCF	chr3:112994680-112994830	GM06990	blood:	n/a	chr3:112994791-112994804
2	CTCF	chr3:112994587-112994985	H1-hESC	embryonic stem cell:	n/a	chr3:112994791-112994804 chr3:112994835-112994843 chr3:112994823-112994844 chr3:112994828-112994846
3	CTCF	chr3:112994680-112994830	GM12864	blood:	n/a	chr3:112994791-112994804
4	RAD21	chr3:112994589-112995046	HepG2	liver:	n/a	chr3:112994830-112994844 chr3:112994835-112994844 chr3:112994826-112994845
5	CTCF	chr3:112994600-112994750	HPAF	blood vessel:	n/a	n/a
6	RAD21	chr3:112994578-112995020	H1-hESC	embryonic stem cell:	n/a	chr3:112994830-112994844 chr3:112994835-112994844 chr3:112994826-112994845
7	CTCF	chr3:112994662-112994961	HepG2	liver:	n/a	chr3:112994791-112994804 chr3:112994835-112994843 chr3:112994823-112994844 chr3:112994828-112994846
8	MAX	chr3:112994657-112995412	ECC-1	luminal epithelium:	n/a	chr3:112994794-112994804
9	ZBTB7A	chr3:112994468-112995482	ECC-1	luminal epithelium:	n/a	n/a
10	CTCF	chr3:112994631-112994969	HepG2	liver:	n/a	chr3:112994791-112994804 chr3:112994835-112994843 chr3:112994823-112994844 chr3:112994828-112994846
11	RAD21	chr3:112994504-112995386	ECC-1	luminal epithelium:	n/a	chr3:112994830-112994844 chr3:112995281-112995294 chr3:112994835-112994844 chr3:112994826-112994845 chr3:112995288-112995302
12	RAD21	chr3:112994650-112995173	H1-hESC	embryonic stem cell:	n/a	chr3:112994830-112994844 chr3:112994835-112994844 chr3:112994826-112994845
13	RAD21	chr3:112994625-112995088	SK-N-SH_RA	brain:	n/a	chr3:112994830-112994844 chr3:112994835-112994844 chr3:112994826-112994845
14	RAD21	chr3:112994655-112995044	IMR90	lung:	n/a	chr3:112994830-112994844 chr3:112994835-112994844 chr3:112994826-112994845
15	MAX	chr3:112994669-112995391	ECC-1	luminal epithelium:	n/a	chr3:112994794-112994804
16	GTF2F1	chr3:112994707-112994734	H1-hESC	embryonic stem cell:	n/a	n/a
17	RAD21	chr3:112994695-112994973	HepG2	liver:	n/a	chr3:112994830-112994844 chr3:112994835-112994844 chr3:112994826-112994845
18	NFIC	chr3:112994595-112995396	ECC-1	luminal epithelium:	n/a	n/a
19	ESR1	chr3:112994708-112995256	ECC-1	luminal epithelium:	n/a	n/a
20	ESR1	chr3:112994626-112995270	ECC-1	luminal epithelium:	n/a	n/a
21	NFIC	chr3:112994547-112995381	ECC-1	luminal epithelium:	n/a	n/a
22	CTCF	chr3:112994700-112994850	GM12871	blood:	n/a	chr3:112994791-112994804 chr3:112994835-112994843 chr3:112994823-112994844 chr3:112994828-112994846
23	EP300	chr3:112994691-112995500	ECC-1	luminal epithelium:	n/a	n/a
24	ZBTB7A	chr3:112994550-112995064	ECC-1	luminal epithelium:	n/a	n/a
25	CTCF	chr3:112994620-112994770	NHLF	lung:	n/a	n/a
26	FOXM1	chr3:112994567-112995495	ECC-1	luminal epithelium:	n/a	n/a
27	ESR1	chr3:112994650-112995310	ECC-1	luminal epithelium:	n/a	n/a
28	CTCF	chr3:112994600-112994750	HAc	cerebellar:	n/a	n/a
29	TEAD4	chr3:112994619-112995426	ECC-1	luminal epithelium:	n/a	n/a
30	ESR1	chr3:112994562-112995380	ECC-1	luminal epithelium:	n/a	n/a
31	RAD21	chr3:112994555-112995155	H1-hESC	embryonic stem cell:	n/a	chr3:112994830-112994844 chr3:112994835-112994844 chr3:112994826-112994845
32	RAD21	chr3:112994635-112995190	ECC-1	luminal epithelium:	n/a	chr3:112994830-112994844 chr3:112994835-112994844 chr3:112994826-112994845
33	CTCF	chr3:112994658-112995033	H1-hESC	embryonic stem cell:	n/a	chr3:112994791-112994804 chr3:112994835-112994843 chr3:112994823-112994844 chr3:112994828-112994846
34	CTCF	chr3:112994590-112995116	MCF-7	breast:	n/a	chr3:112994791-112994804 chr3:112995057-112995078 chr3:112994835-112994843 chr3:112994823-112994844 chr3:112994828-112994846 chr3:112995055-112995073
35	RAD21	chr3:112994599-112995150	MCF-7	breast:	n/a	chr3:112994830-112994844 chr3:112994835-112994844 chr3:112994826-112994845
36	RAD21	chr3:112994649-112994954	HepG2	liver:	n/a	chr3:112994830-112994844 chr3:112994835-112994844 chr3:112994826-112994845
37	EP300	chr3:112994544-112995574	ECC-1	luminal epithelium:	n/a	n/a
38	KAP1	chr3:112994657-112995151	U2OS	brain:	n/a	n/a
39	RFX5	chr3:112994709-112994851	HepG2	liver:	n/a	n/a
40	CTCF	chr3:112994565-112995154	MCF-7	breast:	n/a	chr3:112994791-112994804 chr3:112995057-112995078 chr3:112994835-112994843 chr3:112994823-112994844 chr3:112994828-112994846 chr3:112995055-112995073
41	POLR2A	chr3:112994661-112995352	ECC-1	luminal epithelium:	n/a	n/a
42	TCF12	chr3:112994586-112995538	ECC-1	luminal epithelium:	n/a	chr3:112994836-112994846 chr3:112995129-112995137
43	TCF12	chr3:112994549-112995438	ECC-1	luminal epithelium:	n/a	chr3:112994836-112994846 chr3:112995129-112995137

No.	Distal block	Cell Line	Cell type
1	chr3:112854694..112855593-chr3:112994517..112995397,2	MCF-7	breast:
2	chr3:112854651..112855751-chr3:112994357..112995381,6	MCF-7	breast:
3	chr3:112770020..112770678-chr3:112994428..112995328,4	MCF-7	breast:
4	chr3:112994340..112996390-chr3:112999455..113002856,3	MCF-7	breast:
5	chr3:112769779..112770713-chr3:112994422..112995284,3	MCF-7	breast:

Variant related genes	Relation type
BOC	TF binding region

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1499898	0.82[ASN][1000 genomes]
rs16845106	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16860709	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16860720	0.82[ASN][1000 genomes]
rs17255950	1.00[AFR][1000 genomes]
rs17256551	1.00[AFR][1000 genomes]
rs17256752	1.00[AFR][1000 genomes]
rs17320040	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17320242	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17322613	1.00[AFR][1000 genomes]
rs2291412	1.00[AFR][1000 genomes]
rs2399476	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34600669	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41271353	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56772417	1.00[AFR][1000 genomes]
rs57104308	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57115529	1.00[AFR][1000 genomes]
rs57164268	1.00[AFR][1000 genomes]
rs58905600	1.00[AFR][1000 genomes]
rs58988763	1.00[AFR][1000 genomes]
rs59493419	1.00[AFR][1000 genomes]
rs59590258	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59742486	1.00[AFR][1000 genomes]
rs60070011	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60582065	1.00[AFR][1000 genomes]
rs60697865	1.00[AFR][1000 genomes]
rs60940543	1.00[AFR][1000 genomes]
rs61035513	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61594119	1.00[AFR][1000 genomes]
rs735	1.00[AFR][1000 genomes]
rs9820139	0.86[ASN][1000 genomes]
rs9832953	0.88[ASN][1000 genomes]
rs9849714	0.82[ASN][1000 genomes]
rs9855011	0.82[ASN][1000 genomes]
rs9872998	0.86[ASN][1000 genomes]
rs9878424	0.86[ASN][1000 genomes]
rs998647	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs999365	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3431441	chr3:112453467-113213252	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv829677	chr3:112857075-113038987	Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv1013506	chr3:112890608-113680951	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	nsv877348	chr3:112914756-113012509	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112969000-112995200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr3:112973600-112997200	Weak transcription	Colonic Mucosa	Colon
3	chr3:112983800-112995000	Weak transcription	Lung	lung
4	chr3:112984800-112998400	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr3:112984800-113016400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr3:112987800-112996000	Enhancers	Pancreas	Pancrea
7	chr3:112988000-113003000	Strong transcription	Placenta Amnion	Placenta Amnion
8	chr3:112988400-112996800	Weak transcription	Placenta	Placenta
9	chr3:112989000-112997000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr3:112990200-112994800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr3:112990400-113036000	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr3:112990600-113004000	Weak transcription	NHEK	skin
13	chr3:112991600-112995000	Weak transcription	Aorta	Aorta
14	chr3:112991600-112995000	Weak transcription	K562	blood
15	chr3:112991800-112995000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr3:112991800-113006400	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr3:112992400-112995200	Genic enhancers	Fetal Muscle Leg	muscle
18	chr3:112992800-112995000	Genic enhancers	Fetal Muscle Trunk	muscle
19	chr3:112993000-112995600	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr3:112993000-112996200	Enhancers	Fetal Thymus	thymus
21	chr3:112993000-112997000	Weak transcription	Fetal Intestine Small	intestine
22	chr3:112993400-112995800	Enhancers	Fetal Brain Male	brain
23	chr3:112993400-112996200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:112993400-112996800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr3:112993400-112997400	Genic enhancers	Fetal Stomach	stomach
26	chr3:112993600-112994800	Enhancers	Brain Inferior Temporal Lobe	brain
27	chr3:112993600-112995000	Enhancers	Brain Cingulate Gyrus	brain
28	chr3:112993600-112995000	Enhancers	Fetal Brain Female	brain
29	chr3:112993600-112995000	Enhancers	HMEC	breast
30	chr3:112993600-112995600	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr3:112993600-112995800	Enhancers	Fetal Kidney	kidney
32	chr3:112993600-112996200	Genic enhancers	Fetal Lung	lung
33	chr3:112993800-112994800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr3:112993800-112994800	Enhancers	Brain Substantia Nigra	brain
35	chr3:112993800-112994800	Enhancers	Skeletal Muscle Male	skeletal muscle
36	chr3:112993800-112996400	Enhancers	Brain Angular Gyrus	brain
37	chr3:112993800-112997000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr3:112993800-113036000	Weak transcription	Right Ventricle	heart
39	chr3:112994000-112994800	Enhancers	Muscle Satellite Cultured Cells	--
40	chr3:112994000-112994800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr3:112994000-112994800	Enhancers	Brain Anterior Caudate	brain
42	chr3:112994000-112995000	Enhancers	Primary monocytes fromperipheralblood	blood
43	chr3:112994000-112995000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr3:112994000-112995000	Enhancers	Brain Germinal Matrix	brain
45	chr3:112994000-112995000	Enhancers	Duodenum Smooth Muscle	Duodenum
46	chr3:112994000-112995200	Enhancers	Primary B cells from peripheral blood	blood
47	chr3:112994000-112995400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr3:112994000-112995400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr3:112994000-112995800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr3:112994000-112995800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links