Variant report

Variant	rs549862148
Chromosome Location	chr12:31744737-31744738
allele	-/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	PAX5	chr12:31744319-31744819	GM12878	blood:	n/a	n/a
2	POLR2A	chr12:31742347-31744772	IMR90	lung:	n/a	n/a
3	POLR2A	chr12:31742595-31744836	GM19193	blood:	n/a	n/a
4	TCF12	chr12:31744267-31745015	SK-N-SH	brain:	n/a	n/a
5	MAX	chr12:31744078-31744751	A549	lung:	n/a	chr12:31744239-31744248
6	RCOR1	chr12:31744357-31744843	K562	blood:	n/a	n/a
7	TAF1	chr12:31743174-31744796	H1-neurons	neurons:	n/a	n/a
8	POLR2A	chr12:31742631-31744748	GM19099	blood:	n/a	n/a
9	POLR2A	chr12:31744622-31744833	K562	blood:	n/a	n/a
10	MTA3	chr12:31744025-31744968	GM12878	blood:	n/a	n/a
11	FOXM1	chr12:31744231-31744796	GM12878	blood:	n/a	n/a
12	BHLHE40	chr12:31742555-31744782	HepG2	liver:	n/a	chr12:31743218-31743231 chr12:31743220-31743229 chr12:31743219-31743228 chr12:31743220-31743229 chr12:31744029-31744045
13	TCF12	chr12:31743881-31744893	A549	lung:	n/a	n/a
14	FOXA1	chr12:31744421-31744865	HepG2	liver:	n/a	n/a
15	FOXA1	chr12:31744548-31744807	T-47D	breast:	n/a	n/a
16	GATA3	chr12:31743700-31745058	A549	lung:	n/a	chr12:31744727-31744736
17	FOXA2	chr12:31744498-31744862	HepG2	liver:	n/a	n/a
18	FOXA2	chr12:31744539-31745028	A549	lung:	n/a	n/a
19	NFIC	chr12:31744177-31744908	GM12878	blood:	n/a	n/a
20	EP300	chr12:31744400-31744875	SK-N-SH_RA	brain:	n/a	chr12:31744769-31744778
21	GATA3	chr12:31744547-31744954	SH-SY5Y	brain:	n/a	chr12:31744727-31744736
22	HA-E2F1	chr12:31744164-31744930	MCF-7	breast:	n/a	n/a
23	RUNX3	chr12:31742495-31744863	GM12878	blood:	n/a	chr12:31743445-31743462
24	POLR2A	chr12:31742652-31744833	HUVEC	blood vessel:	n/a	n/a
25	POLR2A	chr12:31742574-31744772	GM18505	blood:	n/a	n/a
26	POLR2A	chr12:31742530-31744830	H1-neurons	neurons:	n/a	n/a
27	GATA3	chr12:31744305-31745047	SK-N-SH	brain:	n/a	chr12:31744727-31744736
28	FOXA1	chr12:31744415-31744876	HepG2	liver:	n/a	n/a
29	POLR2A	chr12:31742528-31744802	GM12878	blood:	n/a	n/a
30	FOXA1	chr12:31744407-31744873	HepG2	liver:	n/a	n/a
31	POLR2A	chr12:31742626-31744802	GM15510	blood:	n/a	n/a
32	RAD21	chr12:31744613-31744859	SK-N-SH_RA	brain:	n/a	n/a
33	HNF4A	chr12:31742736-31744823	HepG2	liver:	n/a	chr12:31744784-31744797 chr12:31744785-31744797 chr12:31744782-31744800 chr12:31744785-31744798 chr12:31743091-31743106 chr12:31744785-31744798 chr12:31743091-31743106
34	RUNX3	chr12:31744159-31744835	GM12878	blood:	n/a	n/a
35	POLR2A	chr12:31742604-31744772	GM12892	blood:	n/a	n/a
36	CREB1	chr12:31743784-31744935	GM12878	blood:	n/a	n/a
37	POLR2A	chr12:31742615-31744758	GM12878	blood:	n/a	n/a
38	CREB1	chr12:31742538-31744807	HepG2	liver:	n/a	n/a
39	BCL3	chr12:31744072-31744796	A549	lung:	n/a	chr12:31744265-31744278
40	RAD21	chr12:31744477-31744927	SK-N-SH_RA	brain:	n/a	n/a
41	POLR2A	chr12:31742618-31744740	GM18526	blood:	n/a	n/a
42	GATA2	chr12:31744199-31744942	SH-SY5Y	brain:	n/a	chr12:31744727-31744736
43	TBL1XR1	chr12:31744338-31744748	GM12878	blood:	n/a	n/a
44	BCLAF1	chr12:31744256-31744877	GM12878	blood:	n/a	chr12:31744265-31744278
45	FOXA2	chr12:31744361-31744982	A549	lung:	n/a	n/a
46	PBX3	chr12:31744369-31744919	SK-N-SH	brain:	n/a	n/a
47	SIN3AK20	chr12:31744508-31744949	SK-N-SH	brain:	n/a	n/a
48	REST	chr12:31742245-31744985	H1-neurons	neurons:	n/a	chr12:31742853-31742866 chr12:31742978-31742988 chr12:31743585-31743592
49	ATF2	chr12:31744189-31744801	GM12878	blood:	n/a	n/a
50	FOXA1	chr12:31744400-31744908	HepG2	liver:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:31744695-31744745	SK-N-MC	brain:	n/a
2	chr12:31744695-31744745	HIPEpiC	eye:	n/a
3	chr12:31744695-31744745	Caco-2	colon:	n/a
4	chr12:31744695-31744745	PANC-1	pancreas:	n/a
5	chr12:31744695-31744745	IMR90	lung:	fetal
6	chr12:31744695-31744745	HRPEpiC	eye:	n/a
7	chr12:31744695-31744745	AoSMC	blood vessel:	n/a
8	chr12:31744695-31744745	LNCaP	prostate:	n/a
9	chr12:31744695-31744745	HUVEC	blood vessel:	n/a
10	chr12:31744695-31744745	HEEpiC	esophagus:	n/a
11	chr12:31744695-31744745	HEK293	kidney:	embryo
12	chr12:31744695-31744745	ECC-1	luminal epithelium:	n/a
13	chr12:31744695-31744745	SK-N-SH_RA	brain:	n/a
14	chr12:31744695-31744745	GM12891	blood:	n/a
15	chr12:31744695-31744745	RPTEC	kidney:	n/a
16	chr12:31744695-31744745	GM12892	blood:	n/a
17	chr12:31744695-31744745	NB4	blood:	n/a
18	chr12:31744695-31744745	PFSK-1	brain:	n/a
19	chr12:31744695-31744745	AG04450	lung:	fetal
20	chr12:31744695-31744745	SKMC	muscle:	n/a
21	chr12:31744695-31744745	HPAEpiC	pulmonary alveolar:	n/a
22	chr12:31744695-31744745	Hela-S3	cervix:	n/a
23	chr12:31744695-31744745	ovcar-3	ovarian:	n/a
24	chr12:31744695-31744745	U87	brain:	n/a
25	chr12:31744695-31744745	HCPEpiC	choroid plexus:	n/a
26	chr12:31744695-31744745	HRCEpiC	kidney:	n/a
27	chr12:31744695-31744745	MCF10A-Er-Src	breast:	n/a
28	chr12:31744695-31744745	HCM	heart:	n/a
29	chr12:31744695-31744745	BJ	skin:	n/a
30	chr12:31744695-31744745	HCT-116	colon:	n/a
31	chr12:31744695-31744745	HNPCEpiC	eye:	n/a
32	chr12:31744695-31744745	NH-A	brain:	n/a
33	chr12:31744695-31744745	AG04449	skin:	fetal
34	chr12:31744695-31744745	HCF	heart:	n/a
35	chr12:31744695-31744745	HepG2	liver:	n/a
36	chr12:31744695-31744745	T-47D	breast:	n/a
37	chr12:31744695-31744745	GM12878	blood:	n/a
38	chr12:31744695-31744745	HRE	kidney:	n/a
39	chr12:31744695-31744745	HAEpiC	amniotic membrane:	n/a
40	chr12:31744695-31744745	GM19239	blood:	n/a
41	chr12:31744695-31744745	MCF-7	breast:	n/a
42	chr12:31744695-31744745	BE2_C	brain:	n/a
43	chr12:31744695-31744745	AG09319	gingival:	n/a
44	chr12:31744695-31744745	K562	blood:	n/a
45	chr12:31744695-31744745	AG09309	skin:	n/a
46	chr12:31744695-31744745	GM06990	blood:	n/a
47	chr12:31744695-31744745	A549	lung:	n/a
48	chr12:31744695-31744745	NHBE	bronchial:	n/a
49	chr12:31744695-31744745	Hepatocyte	liver:	n/a
50	chr12:31744695-31744745	ProgFib	skin:	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
DENND5B	CpG island
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:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:31741400-31745000	Active TSS	Ovary	ovary
2	chr12:31741600-31744800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr12:31741600-31745000	Active TSS	Fetal Kidney	kidney
4	chr12:31741800-31744800	Active TSS	Brain Cingulate Gyrus	brain
5	chr12:31741800-31745000	Active TSS	Rectal Smooth Muscle	rectum
6	chr12:31742000-31744800	Active TSS	NHDF-Ad	bronchial
7	chr12:31742000-31745000	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr12:31742000-31745000	Active TSS	Right Ventricle	heart
9	chr12:31742200-31744800	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr12:31742200-31744800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr12:31742200-31744800	Active TSS	Duodenum Smooth Muscle	Duodenum
12	chr12:31742200-31744800	Active TSS	NHEK	skin
13	chr12:31742200-31745000	Active TSS	Colon Smooth Muscle	Colon
14	chr12:31742200-31745000	Active TSS	Fetal Brain Female	brain
15	chr12:31742400-31744800	Active TSS	H9 Cell Line	embryonic stem cell
16	chr12:31742400-31744800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr12:31742400-31744800	Active TSS	Psoas Muscle	Psoas
18	chr12:31742400-31745000	Active TSS	Aorta	Aorta
19	chr12:31742600-31744800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr12:31742600-31744800	Active TSS	Gastric	stomach
21	chr12:31742600-31744800	Active TSS	Left Ventricle	heart
22	chr12:31742600-31744800	Active TSS	Stomach Mucosa	stomach
23	chr12:31742800-31744800	Active TSS	Breast Myoepithelial Primary Cells	Breast
24	chr12:31742800-31744800	Bivalent/Poised TSS	Primary T cells from cord blood	blood
25	chr12:31743400-31744800	Bivalent/Poised TSS	Thymus	Thymus
26	chr12:31743600-31744800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr12:31744200-31744800	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
28	chr12:31744200-31744800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
29	chr12:31744200-31744800	Flanking Bivalent TSS/Enh	Primary T killer memory cells from peripheral blood	blood
30	chr12:31744200-31744800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
31	chr12:31744200-31744800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
32	chr12:31744200-31744800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr12:31744200-31744800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr12:31744200-31744800	Active TSS	Fetal Brain Male	brain
35	chr12:31744200-31744800	Active TSS	Fetal Heart	heart
36	chr12:31744200-31744800	Flanking Active TSS	Placenta	Placenta
37	chr12:31744200-31744800	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
38	chr12:31744200-31744800	Flanking Active TSS	Pancreas	Pancrea
39	chr12:31744200-31744800	Flanking Active TSS	HUVEC	blood vessel
40	chr12:31744200-31744800	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
41	chr12:31744200-31744800	Flanking Active TSS	NH-A	brain
42	chr12:31744200-31744800	Flanking Active TSS	NHLF	lung
43	chr12:31744200-31745000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
44	chr12:31744200-31745000	Flanking Active TSS	Primary B cells from peripheral blood	blood
45	chr12:31744200-31745000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr12:31744200-31745000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr12:31744200-31745000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr12:31744200-31745000	Flanking Active TSS	Adipose Nuclei	Adipose
49	chr12:31744200-31745000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
50	chr12:31744200-31745000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links