Variant report

Variant	rs554601468
Chromosome Location	chr12:12714269-12714270
allele	C/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	TBP	chr12:12713627-12714716	GM12878	blood:	n/a	n/a
2	POLR2A	chr12:12713681-12714935	HepG2	liver:	n/a	n/a
3	CTCF	chr12:12714220-12714370	NHDF-neo	bronchial:	n/a	n/a
4	SMC3	chr12:12713758-12714720	Hela-S3	cervix:	n/a	n/a
5	FOXA1	chr12:12713736-12714275	HepG2	liver:	n/a	chr12:12714030-12714045 chr12:12713985-12713997
6	JUND	chr12:12714010-12716138	K562	blood:	n/a	chr12:12715384-12715393 chr12:12715493-12715502
7	POLR2A	chr12:12713706-12714961	GM12878	blood:	n/a	n/a
8	BCLAF1	chr12:12713612-12714768	GM12878	blood:	n/a	chr12:12714732-12714745 chr12:12714735-12714748 chr12:12713831-12713840
9	POLR2A	chr12:12713503-12716782	HepG2	liver:	n/a	n/a
10	CEBPB	chr12:12713926-12714349	K562	blood:	n/a	chr12:12714128-12714139
11	ZBTB7A	chr12:12714188-12716298	ECC-1	luminal epithelium:	n/a	chr12:12715455-12715469 chr12:12714468-12714476 chr12:12715115-12715123
12	MYBL2	chr12:12713667-12714516	HepG2	liver:	n/a	chr12:12713758-12713771
13	POLR2A	chr12:12713801-12715363	Hela-S3	cervix:	n/a	n/a
14	RCOR1	chr12:12713765-12714479	K562	blood:	n/a	n/a
15	POLR2A	chr12:12714003-12714275	K562	blood:	n/a	n/a
16	CUX1	chr12:12713250-12714276	GM12878	blood:	n/a	n/a
17	CEBPB	chr12:12714004-12714771	H1-hESC	embryonic stem cell:	n/a	chr12:12714128-12714139
18	CEBPB	chr12:12713952-12714822	IMR90	lung:	n/a	chr12:12714128-12714139
19	SMC3	chr12:12713628-12714678	GM12878	blood:	n/a	n/a
20	MAZ	chr12:12713940-12716143	K562	blood:	n/a	chr12:12714863-12714872 chr12:12714847-12714857
21	CEBPB	chr12:12713910-12714398	MCF-7	breast:	n/a	chr12:12714128-12714139
22	NFYB	chr12:12713965-12714377	GM12878	blood:	n/a	n/a
23	CEBPB	chr12:12713887-12714323	HepG2	liver:	n/a	chr12:12714128-12714139
24	E2F4	chr12:12714080-12714280	MCF10A-Er-Src	breast:	n/a	n/a
25	POLR2A	chr12:12713986-12716119	HUVEC	blood vessel:	n/a	n/a
26	BHLHE40	chr12:12714066-12714708	K562	blood:	n/a	n/a
27	POLR2A	chr12:12714011-12714334	HepG2	liver:	n/a	n/a
28	CEBPB	chr12:12713894-12714807	A549	lung:	n/a	chr12:12714128-12714139
29	FOS	chr12:12713960-12714325	MCF10A-Er-Src	breast:	n/a	n/a
30	YY1	chr12:12714003-12714293	GM12878	blood:	n/a	n/a
31	MAZ	chr12:12713817-12714782	GM12878	blood:	n/a	n/a
32	SPI1	chr12:12713486-12714432	GM12878	blood:	n/a	chr12:12713831-12713840
33	EP300	chr12:12713682-12714659	GM12878	blood:	n/a	chr12:12714007-12714021 chr12:12714126-12714140 chr12:12713910-12713924 chr12:12713901-12713915
34	HDAC2	chr12:12713749-12714297	HepG2	liver:	n/a	chr12:12714143-12714157 chr12:12713913-12713927 chr12:12713988-12713997 chr12:12713909-12713923
35	HDAC2	chr12:12713720-12714295	HepG2	liver:	n/a	chr12:12714143-12714157 chr12:12713913-12713927 chr12:12713988-12713997 chr12:12713909-12713923
36	PML	chr12:12713634-12714946	GM12878	blood:	n/a	n/a
37	CHD1	chr12:12711450-12716107	GM12878	blood:	n/a	n/a
38	CHD1	chr12:12713235-12714685	H1-hESC	embryonic stem cell:	n/a	n/a
39	SMARCC2	chr12:12713739-12714796	Hela-S3	cervix:	n/a	n/a
40	RAD21	chr12:12713777-12714360	Hela-S3	cervix:	n/a	n/a
41	CEBPB	chr12:12713877-12714903	ECC-1	luminal epithelium:	n/a	chr12:12714128-12714139
42	POLR2A	chr12:12713421-12715350	GM12891	blood:	n/a	n/a
43	POLR2A	chr12:12713382-12716397	GM12878	blood:	n/a	n/a
44	BRCA1	chr12:12713877-12714319	HepG2	liver:	n/a	n/a
45	RUNX3	chr12:12713632-12714760	GM12878	blood:	n/a	n/a
46	POLR2A	chr12:12713620-12716156	GM18505	blood:	n/a	n/a
47	FOXA2	chr12:12713694-12714713	HepG2	liver:	n/a	chr12:12713985-12713997
48	MAX	chr12:12713746-12715418	A549	lung:	n/a	chr12:12714863-12714872 chr12:12714847-12714857
49	FOS	chr12:12713991-12714333	MCF10A-Er-Src	breast:	n/a	n/a
50	BCLAF1	chr12:12713562-12715025	GM12878	blood:	n/a	chr12:12714772-12714785 chr12:12714841-12714854 chr12:12714732-12714745 chr12:12714735-12714748 chr12:12713831-12713840

No.	Distal block	Cell Line	Cell type
1	chr12:12418062..12421378-chr12:12712958..12715949,4	MCF-7	breast:
2	chr12:12634486..12639853-chr12:12714024..12717789,5	K562	blood:
3	chr12:12713858..12718896-chr12:12719623..12723320,7	MCF-7	breast:
4	chr12:12710433..12719642-chr12:12755652..12767678,23	MCF-7	breast:
5	chr12:12712251..12716973-chr12:12867058..12873344,10	MCF-7	breast:
6	chr12:12714157..12716777-chr12:12764288..12766468,3	MCF-7	breast:
7	chr12:12672602..12674761-chr12:12714230..12715790,2	MCF-7	breast:
8	chr12:12712910..12717920-chr12:12867983..12871802,5	K562	blood:
9	chr12:12712965..12715376-chr12:12848428..12850169,2	K562	blood:
10	chr12:12713075..12717194-chr12:12718362..12721939,6	K562	blood:
11	chr12:12603843..12606415-chr12:12711459..12714793,4	MCF-7	breast:
12	chr12:12713899..12715883-chr12:12875674..12879074,4	MCF-7	breast:
13	chr12:12711165..12717532-chr12:12865354..12880919,24	MCF-7	breast:
14	chr12:12713736..12716645-chr12:14925588..14929665,3	MCF-7	breast:
15	chr12:12502650..12504579-chr12:12713839..12715957,2	MCF-7	breast:
16	chr12:12713891..12716367-chr3:161087265..161090021,2	MCF-7	breast:
17	chr12:12672853..12675163-chr12:12712393..12714277,2	K562	blood:
18	chr12:12713685..12716948-chr12:12760123..12768151,9	K562	blood:
19	chr12:12713534..12716816-chr12:12876902..12880504,5	K562	blood:
20	chr12:12713878..12715518-chr12:14922092..14923933,2	MCF-7	breast:
21	chr12:12509167..12512867-chr12:12713185..12715471,5	MCF-7	breast:
22	chr12:12507988..12510235-chr12:12714031..12716523,2	MCF-7	breast:

Variant related genes	Relation type
DUSP16	TF binding region
ENSG00000197837	Chromatin interaction
ENSG00000183150	Chromatin interaction
ENSG00000246705	Chromatin interaction
ENSG00000205791	Chromatin interaction
ENSG00000111261	Chromatin interaction
ENSG00000111276	Chromatin interaction
ENSG00000271370	Chromatin interaction
ENSG00000111269	Chromatin interaction
ENSG00000111266	Chromatin interaction
ENSG00000196542	Chromatin interaction
ENSG00000178878	Chromatin interaction
ENSG00000256658	Chromatin interaction
ENSG00000165714	Chromatin interaction
ENSG00000240424	Chromatin interaction
ENSG00000255670	Chromatin interaction
ENSG00000070018	Chromatin interaction

Extended variants
information (count: 4 )
Associated
traits (count: 0)

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	esv2758295	chr12:12620654-12783124	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	esv2759880	chr12:12620654-12783124	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv898811	chr12:12655443-12928295	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	esv3325054	chr12:12713710-12717058	Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12688200-12714400	Weak transcription	Gastric	stomach
2	chr12:12706600-12714400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr12:12711400-12716000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
4	chr12:12711600-12716000	Active TSS	GM12878-XiMat	blood
5	chr12:12711600-12716200	Active TSS	Liver	Liver
6	chr12:12711600-12716200	Active TSS	Duodenum Mucosa	Duodenum
7	chr12:12711600-12716200	Active TSS	Rectal Mucosa Donor 29	rectum
8	chr12:12712000-12716000	Active TSS	Breast Myoepithelial Primary Cells	Breast
9	chr12:12712000-12716000	Active TSS	Fetal Intestine Large	intestine
10	chr12:12712000-12716200	Active TSS	Fetal Intestine Small	intestine
11	chr12:12712200-12716200	Active TSS	HUES6 Cell Line	embryonic stem cell
12	chr12:12712400-12714800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
13	chr12:12712600-12716000	Active TSS	H1 Cell Line	embryonic stem cell
14	chr12:12712600-12716000	Active TSS	H9 Cell Line	embryonic stem cell
15	chr12:12712600-12716000	Active TSS	Colonic Mucosa	Colon
16	chr12:12712600-12716000	Active TSS	Fetal Brain Female	brain
17	chr12:12712600-12716000	Active TSS	Thymus	Thymus
18	chr12:12712600-12716000	Active TSS	K562	blood
19	chr12:12712600-12716200	Active TSS	NHLF	lung
20	chr12:12712800-12714600	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
21	chr12:12712800-12716000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr12:12712800-12716000	Active TSS	Brain Anterior Caudate	brain
23	chr12:12712800-12716000	Active TSS	Fetal Stomach	stomach
24	chr12:12712800-12716200	Active TSS	Brain Cingulate Gyrus	brain
25	chr12:12712800-12716400	Active TSS	HUES48 Cell Line	embryonic stem cell
26	chr12:12712800-12716400	Active TSS	Fetal Muscle Trunk	muscle
27	chr12:12712800-12716400	Active TSS	Right Atrium	heart
28	chr12:12712800-12716800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr12:12713000-12716000	Active TSS	iPS-18 Cell Line	embryonic stem cell
30	chr12:12713000-12716000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
31	chr12:12713000-12716000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr12:12713000-12716000	Active TSS	Fetal Muscle Leg	muscle
33	chr12:12713000-12716000	Active TSS	Stomach Smooth Muscle	stomach
34	chr12:12713000-12716200	Active TSS	ES-I3 Cell Line	embryonic stem cell
35	chr12:12713000-12716200	Active TSS	iPS-20b Cell Line	embryonic stem cell
36	chr12:12713000-12716200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr12:12713200-12714600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr12:12713200-12716000	Active TSS	iPS-15b Cell Line	embryonic stem cell
39	chr12:12713200-12716200	Active TSS	Brain Hippocampus Middle	brain
40	chr12:12713200-12716400	Active TSS	Pancreatic Islets	Pancreatic Islet
41	chr12:12713200-12716600	Active TSS	Brain Angular Gyrus	brain
42	chr12:12713400-12714400	Flanking Active TSS	Adipose Nuclei	Adipose
43	chr12:12713400-12714600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
44	chr12:12713400-12714800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr12:12713400-12716000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr12:12713400-12716400	Active TSS	Aorta	Aorta
47	chr12:12713400-12716400	Active TSS	Brain Inferior Temporal Lobe	brain
48	chr12:12713400-12716400	Active TSS	Psoas Muscle	Psoas
49	chr12:12713400-12716400	Active TSS	Right Ventricle	heart
50	chr12:12713600-12714400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links