Variant report

Variant	rs547997660
Chromosome Location	chr12:31744864-31744865
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	TCF12	chr12:31744267-31745015	SK-N-SH	brain:	n/a	n/a
2	CTCF	chr12:31744800-31744950	AG10803	skin:	n/a	n/a
3	MTA3	chr12:31744025-31744968	GM12878	blood:	n/a	n/a
4	CTCF	chr12:31744820-31744970	HCPEpiC	choroid plexus:	n/a	n/a
5	TCF12	chr12:31743881-31744893	A549	lung:	n/a	n/a
6	FOXA1	chr12:31744421-31744865	HepG2	liver:	n/a	n/a
7	GATA3	chr12:31743700-31745058	A549	lung:	n/a	chr12:31744727-31744736
8	FOXA2	chr12:31744539-31745028	A549	lung:	n/a	n/a
9	NFIC	chr12:31744177-31744908	GM12878	blood:	n/a	n/a
10	EP300	chr12:31744400-31744875	SK-N-SH_RA	brain:	n/a	chr12:31744769-31744778
11	GATA3	chr12:31744547-31744954	SH-SY5Y	brain:	n/a	chr12:31744727-31744736
12	HA-E2F1	chr12:31744164-31744930	MCF-7	breast:	n/a	n/a
13	GATA3	chr12:31744305-31745047	SK-N-SH	brain:	n/a	chr12:31744727-31744736
14	FOXA1	chr12:31744415-31744876	HepG2	liver:	n/a	n/a
15	FOXA1	chr12:31744407-31744873	HepG2	liver:	n/a	n/a
16	CREB1	chr12:31743784-31744935	GM12878	blood:	n/a	n/a
17	RAD21	chr12:31744477-31744927	SK-N-SH_RA	brain:	n/a	n/a
18	GATA2	chr12:31744199-31744942	SH-SY5Y	brain:	n/a	chr12:31744727-31744736
19	BCLAF1	chr12:31744256-31744877	GM12878	blood:	n/a	chr12:31744265-31744278
20	FOXA2	chr12:31744361-31744982	A549	lung:	n/a	n/a
21	PBX3	chr12:31744369-31744919	SK-N-SH	brain:	n/a	n/a
22	SIN3AK20	chr12:31744508-31744949	SK-N-SH	brain:	n/a	n/a
23	REST	chr12:31742245-31744985	H1-neurons	neurons:	n/a	chr12:31742853-31742866 chr12:31742978-31742988 chr12:31743585-31743592
24	FOXA1	chr12:31744400-31744908	HepG2	liver:	n/a	n/a
25	MTA3	chr12:31744215-31745034	GM12878	blood:	n/a	n/a
26	MAX	chr12:31742429-31745066	A549	lung:	n/a	chr12:31744239-31744248
27	MAX	chr12:31742561-31744891	HepG2	liver:	n/a	chr12:31744239-31744248
28	GATA3	chr12:31744390-31745048	SK-N-SH	brain:	n/a	chr12:31744727-31744736
29	PBX3	chr12:31744287-31744976	SK-N-SH	brain:	n/a	n/a
30	MAZ	chr12:31742339-31745036	IMR90	lung:	n/a	chr12:31744239-31744248
31	TCF12	chr12:31744341-31745017	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:31741307..31745552-chr12:31748528..31751513,3	MCF-7	breast:
2	chr12:31477521..31479099-chr12:31743621..31745412,2	K562	blood:
3	chr12:31645308..31649621-chr12:31742506..31745309,6	MCF-7	breast:

Variant related genes	Relation type
DENND5B	TF binding region
ENSG00000170456	Chromatin interaction
ENSG00000231788	Chromatin interaction
ENSG00000139146	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

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	nsv1041877	chr12:31009451-31809254	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv541440	chr12:31009451-31809254	ZNF genes & repeats Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
3	esv1836923	chr12:31539122-31761172	Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	esv2760267	chr12:31626732-31909908	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
5	nsv898965	chr12:31631819-31771689	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv832365	chr12:31642811-31808532	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	esv1797962	chr12:31733044-31761172	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	esv3371967	chr12:31741685-31745983	Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	esv3375615	chr12:31742710-31745258	Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	esv1804747	chr12:31743194-31748491	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	esv1840310	chr12:31743194-31750986	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 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	chr12:31741400-31745000	Active TSS	Ovary	ovary
2	chr12:31741600-31745000	Active TSS	Fetal Kidney	kidney
3	chr12:31741800-31745000	Active TSS	Rectal Smooth Muscle	rectum
4	chr12:31742000-31745000	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr12:31742000-31745000	Active TSS	Right Ventricle	heart
6	chr12:31742200-31745000	Active TSS	Colon Smooth Muscle	Colon
7	chr12:31742200-31745000	Active TSS	Fetal Brain Female	brain
8	chr12:31742400-31745000	Active TSS	Aorta	Aorta
9	chr12:31744200-31745000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
10	chr12:31744200-31745000	Flanking Active TSS	Primary B cells from peripheral blood	blood
11	chr12:31744200-31745000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr12:31744200-31745000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr12:31744200-31745000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr12:31744200-31745000	Flanking Active TSS	Adipose Nuclei	Adipose
15	chr12:31744200-31745000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
16	chr12:31744200-31745000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
17	chr12:31744400-31745000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr12:31744400-31745000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr12:31744400-31745000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr12:31744400-31745000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr12:31744400-31745000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr12:31744400-31745000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr12:31744400-31745000	Flanking Active TSS	Primary B cells from cord blood	blood
24	chr12:31744400-31745000	Flanking Active TSS	Primary hematopoietic stem cells	blood
25	chr12:31744400-31745000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr12:31744400-31745000	Flanking Active TSS	Liver	Liver
27	chr12:31744400-31745000	Flanking Active TSS	Brain Angular Gyrus	brain
28	chr12:31744400-31745000	Flanking Active TSS	Duodenum Mucosa	Duodenum
29	chr12:31744400-31745000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
30	chr12:31744400-31745000	Flanking Active TSS	Fetal Muscle Leg	muscle
31	chr12:31744400-31745000	Active TSS	Right Atrium	heart
32	chr12:31744400-31745000	Enhancers	Sigmoid Colon	Sigmoid Colon
33	chr12:31744400-31745000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
34	chr12:31744400-31745000	Flanking Active TSS	GM12878-XiMat	blood
35	chr12:31744400-31745000	Flanking Active TSS	HSMMtube	muscle
36	chr12:31744400-31745000	Flanking Active TSS	Osteobl	bone
37	chr12:31744400-31745200	Flanking Active TSS	Fetal Intestine Small	intestine
38	chr12:31744600-31745000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr12:31744600-31745000	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
40	chr12:31744600-31745000	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
41	chr12:31744600-31745000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr12:31744600-31745000	Flanking Active TSS	Brain Anterior Caudate	brain
43	chr12:31744600-31745000	Flanking Active TSS	Brain Germinal Matrix	brain
44	chr12:31744600-31745000	Flanking Active TSS	Fetal Intestine Large	intestine
45	chr12:31744600-31745000	Flanking Active TSS	Stomach Smooth Muscle	stomach
46	chr12:31744600-31745400	Enhancers	Placenta Amnion	Placenta Amnion
47	chr12:31744600-31747800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr12:31744800-31745000	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
49	chr12:31744800-31745000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
50	chr12:31744800-31745000	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links