Variant report

Variant	rs775227
Chromosome Location	chr3:112995074-112995075
allele	A/C
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	chr3:112995019-112995133	MCF-7	breast:	n/a	chr3:112995057-112995078 chr3:112995055-112995073
2	CTCF	chr3:112994960-112995110	HPAF	blood vessel:	n/a	chr3:112995057-112995078 chr3:112995055-112995073
3	CTCF	chr3:112994975-112995144	GM19238	blood:	n/a	chr3:112995057-112995078 chr3:112995055-112995073
4	NR3C1	chr3:112994767-112995287	ECC-1	luminal epithelium:	n/a	n/a
5	POLR2A	chr3:112995062-112995249	MCF10A-Er-Src	breast:	n/a	n/a
6	MAZ	chr3:112994926-112995079	K562	blood:	n/a	n/a
7	MXI1	chr3:112995022-112995163	GM12878	blood:	n/a	n/a
8	POLR2A	chr3:112995067-112995380	Gliobla	brain:	n/a	n/a
9	CTCF	chr3:112995040-112995190	GM12864	blood:	n/a	chr3:112995057-112995078 chr3:112995055-112995073
10	CTCF	chr3:112994980-112995130	SAEC	small airway:	n/a	chr3:112995057-112995078 chr3:112995055-112995073
11	CTCF	chr3:112995000-112995150	MCF-7	breast:	n/a	chr3:112995057-112995078 chr3:112995055-112995073
12	POLR2A	chr3:112995020-112995536	GM12892	blood:	n/a	n/a
13	EBF1	chr3:112994913-112995310	GM12878	blood:	n/a	n/a
14	ARID3A	chr3:112994883-112995237	HepG2	liver:	n/a	chr3:112995046-112995061
15	CTCF	chr3:112994960-112995110	HEEpiC	esophagus:	n/a	chr3:112995057-112995078 chr3:112995055-112995073
16	CTCF	chr3:112994940-112995090	GM12873	blood:	n/a	chr3:112995057-112995078 chr3:112995055-112995073
17	CTCF	chr3:112995027-112995088	LNCaP	prostate:	n/a	chr3:112995057-112995078 chr3:112995055-112995073
18	MAX	chr3:112994657-112995412	ECC-1	luminal epithelium:	n/a	chr3:112994794-112994804
19	SPI1	chr3:112994994-112995650	GM12891	blood:	n/a	chr3:112995530-112995539 chr3:112995265-112995274
20	SPI1	chr3:112994871-112995720	GM12878	blood:	n/a	chr3:112995530-112995539 chr3:112995265-112995274
21	CTCF	chr3:112994960-112995110	WERI-Rb-1	eye:	n/a	chr3:112995057-112995078 chr3:112995055-112995073
22	CTCF	chr3:112994940-112995090	AG04450	lung:	n/a	chr3:112995057-112995078 chr3:112995055-112995073
23	CTCF	chr3:112995000-112995150	GM12869	blood:	n/a	chr3:112995057-112995078 chr3:112995055-112995073
24	ZBTB7A	chr3:112994468-112995482	ECC-1	luminal epithelium:	n/a	n/a
25	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
26	CTCF	chr3:112995016-112995141	GM12892	blood:	n/a	chr3:112995057-112995078 chr3:112995055-112995073
27	BHLHE40	chr3:112995059-112995092	GM12878	blood:	n/a	n/a
28	CTCF	chr3:112995011-112995140	Gliobla	brain:	n/a	chr3:112995057-112995078 chr3:112995055-112995073
29	POLR2A	chr3:112994906-112995372	U87	brain:	n/a	n/a
30	CTCF	chr3:112995031-112995140	MCF-7	breast:	n/a	chr3:112995057-112995078 chr3:112995055-112995073
31	RAD21	chr3:112994650-112995173	H1-hESC	embryonic stem cell:	n/a	chr3:112994830-112994844 chr3:112994835-112994844 chr3:112994826-112994845
32	RUNX3	chr3:112994916-112995332	GM12878	blood:	n/a	n/a
33	CTCF	chr3:112995020-112995170	AG10803	skin:	n/a	chr3:112995057-112995078 chr3:112995055-112995073
34	CTCF	chr3:112995020-112995170	GM12868	blood:	n/a	chr3:112995057-112995078 chr3:112995055-112995073
35	CTCF	chr3:112994981-112995189	GM19239	blood:	n/a	chr3:112995057-112995078 chr3:112995055-112995073
36	RAD21	chr3:112994625-112995088	SK-N-SH_RA	brain:	n/a	chr3:112994830-112994844 chr3:112994835-112994844 chr3:112994826-112994845
37	RCOR1	chr3:112994841-112995153	K562	blood:	n/a	n/a
38	CTCF	chr3:112995040-112995190	WI-38	lung:	n/a	chr3:112995057-112995078 chr3:112995055-112995073
39	CTCF	chr3:112994980-112995130	GM12872	blood:	n/a	chr3:112995057-112995078 chr3:112995055-112995073
40	CTCF	chr3:112994946-112995146	GM19240	blood:	n/a	chr3:112995057-112995078 chr3:112995055-112995073
41	MYC	chr3:112994949-112995186	MCF10A-Er-Src	breast:	n/a	n/a
42	SPI1	chr3:112995071-112995702	GM12891	blood:	n/a	chr3:112995530-112995539 chr3:112995265-112995274
43	PBX3	chr3:112995020-112995283	GM12878	blood:	n/a	n/a
44	MAX	chr3:112994669-112995391	ECC-1	luminal epithelium:	n/a	chr3:112994794-112994804
45	CTCF	chr3:112995023-112995122	ProgFib	skin:	n/a	chr3:112995057-112995078 chr3:112995055-112995073
46	CTCF	chr3:112995000-112995150	GM12866	blood:	n/a	chr3:112995057-112995078 chr3:112995055-112995073
47	CTCF	chr3:112995000-112995150	HAc	cerebellar:	n/a	chr3:112995057-112995078 chr3:112995055-112995073
48	NFIC	chr3:112994595-112995396	ECC-1	luminal epithelium:	n/a	n/a
49	CTCF	chr3:112995051-112995126	MCF-7	breast:	n/a	chr3:112995057-112995078 chr3:112995055-112995073
50	CTCF	chr3:112994996-112995136	MCF-7	breast:	n/a	chr3:112995057-112995078 chr3:112995055-112995073

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: 14 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs13093350	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13094203	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2291905	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs2650100	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34239722	0.85[EUR][1000 genomes]
rs35341359	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41271355	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56163361	0.85[EUR][1000 genomes]
rs66518523	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs808951	1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.97[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

Variant related diseases (count:1)

Disease	PMID	Source
Dental caries	23259602	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs775227	BOC	cis	parietal	SCAN

Chromatin state (count:106 , 50 per page) page: 1 2 3

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	chr3:112984800-112998400	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr3:112984800-113016400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr3:112987800-112996000	Enhancers	Pancreas	Pancrea
6	chr3:112988000-113003000	Strong transcription	Placenta Amnion	Placenta Amnion
7	chr3:112988400-112996800	Weak transcription	Placenta	Placenta
8	chr3:112989000-112997000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr3:112990400-113036000	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr3:112990600-113004000	Weak transcription	NHEK	skin
11	chr3:112991800-113006400	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr3:112992400-112995200	Genic enhancers	Fetal Muscle Leg	muscle
13	chr3:112993000-112995600	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr3:112993000-112996200	Enhancers	Fetal Thymus	thymus
15	chr3:112993000-112997000	Weak transcription	Fetal Intestine Small	intestine
16	chr3:112993400-112995800	Enhancers	Fetal Brain Male	brain
17	chr3:112993400-112996200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr3:112993400-112996800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr3:112993400-112997400	Genic enhancers	Fetal Stomach	stomach
20	chr3:112993600-112995600	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr3:112993600-112995800	Enhancers	Fetal Kidney	kidney
22	chr3:112993600-112996200	Genic enhancers	Fetal Lung	lung
23	chr3:112993800-112996400	Enhancers	Brain Angular Gyrus	brain
24	chr3:112993800-112997000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr3:112993800-113036000	Weak transcription	Right Ventricle	heart
26	chr3:112994000-112995200	Enhancers	Primary B cells from peripheral blood	blood
27	chr3:112994000-112995400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr3:112994000-112995400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr3:112994000-112995800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr3:112994000-112995800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr3:112994200-112995200	Enhancers	H1 Cell Line	embryonic stem cell
32	chr3:112994200-112995200	Enhancers	Fetal Intestine Large	intestine
33	chr3:112994200-112995400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
34	chr3:112994200-112995600	Enhancers	iPS-20b Cell Line	embryonic stem cell
35	chr3:112994200-112997800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
36	chr3:112994400-112995200	Enhancers	HUES64 Cell Line	embryonic stem cell
37	chr3:112994400-112995400	Enhancers	iPS-18 Cell Line	embryonic stem cell
38	chr3:112994400-112995400	Weak transcription	Liver	Liver
39	chr3:112994400-112995600	Flanking Active TSS	HepG2	liver
40	chr3:112994400-112996400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
41	chr3:112994600-112995200	Enhancers	HUES48 Cell Line	embryonic stem cell
42	chr3:112994600-112995200	Enhancers	HUES6 Cell Line	embryonic stem cell
43	chr3:112994600-112995200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr3:112994600-112995200	Enhancers	Primary hematopoietic stem cells	blood
45	chr3:112994600-112995200	Enhancers	Ovary	ovary
46	chr3:112994600-112995200	Enhancers	Rectal Mucosa Donor 29	rectum
47	chr3:112994600-112995200	Enhancers	Rectal Mucosa Donor 31	rectum
48	chr3:112994600-112995200	Enhancers	Right Atrium	heart
49	chr3:112994600-112995400	Enhancers	ES-I3 Cell Line	embryonic stem cell
50	chr3:112994600-112995400	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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