Variant report

Variant	rs375913628
Chromosome Location	chr12:51663418-51663419
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	chr12:51662895-51665050	SK-N-SH	brain:	n/a	chr12:51663487-51663505 chr12:51664248-51664269 chr12:51664255-51664268 chr12:51663212-51663233 chr12:51663489-51663510 chr12:51663641-51663654 chr12:51663490-51663499 chr12:51664253-51664271
2	MAX	chr12:51663212-51664801	HepG2	liver:	n/a	n/a
3	RAD21	chr12:51663382-51663650	GM12878	blood:	n/a	chr12:51663488-51663507 chr12:51663489-51663498
4	CTCF	chr12:51663265-51663689	HepG2	liver:	n/a	chr12:51663487-51663505 chr12:51663489-51663510 chr12:51663641-51663654 chr12:51663490-51663499
5	CTCF	chr12:51663400-51663550	AG04449	skin:	n/a	chr12:51663487-51663505 chr12:51663489-51663510 chr12:51663490-51663499
6	TAF1	chr12:51663362-51663744	H1-hESC	embryonic stem cell:	n/a	n/a
7	CTCF	chr12:51663400-51663550	HMEC	breast:	n/a	chr12:51663487-51663505 chr12:51663489-51663510 chr12:51663490-51663499
8	RAD21	chr12:51663345-51663675	SK-N-SH_RA	brain:	n/a	chr12:51663488-51663507 chr12:51663489-51663498
9	CTCF	chr12:51663380-51663530	HFF	foreskin:	n/a	chr12:51663487-51663505 chr12:51663489-51663510 chr12:51663490-51663499
10	NR2F2	chr12:51663218-51664405	MCF-7	breast:	n/a	n/a
11	TCF12	chr12:51663245-51664924	ECC-1	luminal epithelium:	n/a	chr12:51663493-51663500 chr12:51664606-51664613 chr12:51663955-51663962
12	TEAD4	chr12:51663157-51663682	K562	blood:	n/a	n/a
13	CTCF	chr12:51663340-51663490	HRPEpiC	eye:	n/a	n/a
14	CTCF	chr12:51663400-51663550	HAc	cerebellar:	n/a	chr12:51663487-51663505 chr12:51663489-51663510 chr12:51663490-51663499
15	CTCF	chr12:51663400-51663550	SK-N-SH_RA	brain:	n/a	chr12:51663487-51663505 chr12:51663489-51663510 chr12:51663490-51663499
16	CTCF	chr12:51663400-51663550	SAEC	small airway:	n/a	chr12:51663487-51663505 chr12:51663489-51663510 chr12:51663490-51663499
17	CTCF	chr12:51663280-51663686	K562	blood:	n/a	chr12:51663487-51663505 chr12:51663489-51663510 chr12:51663641-51663654 chr12:51663490-51663499
18	SMC3	chr12:51662943-51663709	K562	blood:	n/a	chr12:51663489-51663503 chr12:51663669-51663679
19	EGR1	chr12:51663403-51663806	K562	blood:	n/a	chr12:51663641-51663651 chr12:51663640-51663650 chr12:51663640-51663653 chr12:51663550-51663560 chr12:51663545-51663558
20	CTCF	chr12:51663229-51663734	H1-hESC	embryonic stem cell:	n/a	chr12:51663487-51663505 chr12:51663489-51663510 chr12:51663641-51663654 chr12:51663490-51663499
21	CTCF	chr12:51663393-51663580	Lung_OC	lung:	n/a	chr12:51663487-51663505 chr12:51663489-51663510 chr12:51663490-51663499
22	EGR1	chr12:51663375-51664313	K562	blood:	n/a	chr12:51664012-51664025 chr12:51663641-51663651 chr12:51664103-51664112 chr12:51663640-51663650 chr12:51663640-51663653 chr12:51663864-51663877 chr12:51663550-51663560 chr12:51663545-51663558
23	MAZ	chr12:51663380-51665099	IMR90	lung:	n/a	n/a
24	CTCF	chr12:51663400-51663550	GM12872	blood:	n/a	chr12:51663487-51663505 chr12:51663489-51663510 chr12:51663490-51663499
25	TAF1	chr12:51663391-51663754	K562	blood:	n/a	n/a
26	HDAC2	chr12:51663237-51664438	MCF-7	breast:	n/a	n/a
27	RAD21	chr12:51663190-51663788	ECC-1	luminal epithelium:	n/a	chr12:51663488-51663507 chr12:51663489-51663498
28	RAD21	chr12:51663271-51663706	H1-hESC	embryonic stem cell:	n/a	chr12:51663488-51663507 chr12:51663489-51663498
29	MAX	chr12:51663069-51664971	ECC-1	luminal epithelium:	n/a	n/a
30	E2F6	chr12:51663205-51664411	K562	blood:	n/a	chr12:51664070-51664080 chr12:51664105-51664114 chr12:51663901-51663911
31	RAD21	chr12:51663318-51663672	GM12878	blood:	n/a	chr12:51663488-51663507 chr12:51663489-51663498
32	ATF2	chr12:51663156-51663670	H1-hESC	embryonic stem cell:	n/a	n/a
33	CTCF	chr12:51663281-51663648	K562	blood:	n/a	chr12:51663487-51663505 chr12:51663489-51663510 chr12:51663490-51663499
34	CTCF	chr12:51663375-51663605	GM12891	blood:	n/a	chr12:51663487-51663505 chr12:51663489-51663510 chr12:51663490-51663499
35	ZNF143	chr12:51663353-51663653	GM12878	blood:	n/a	n/a
36	CTCF	chr12:51663359-51663664	T-47D	breast:	n/a	chr12:51663487-51663505 chr12:51663489-51663510 chr12:51663641-51663654 chr12:51663490-51663499
37	RAD21	chr12:51663170-51663807	A549	lung:	n/a	chr12:51663488-51663507 chr12:51663489-51663498
38	SP1	chr12:51663115-51665261	HCT-116	colon:	n/a	chr12:51664015-51664026 chr12:51664015-51664027 chr12:51664205-51664217 chr12:51664105-51664114 chr12:51664206-51664215 chr12:51664015-51664027 chr12:51664202-51664216 chr12:51664206-51664216 chr12:51664205-51664217
39	CTCF	chr12:51663385-51663593	Hela-S3	cervix:	n/a	chr12:51663487-51663505 chr12:51663489-51663510 chr12:51663490-51663499
40	CTCF	chr12:51663392-51663593	Fibrobl	skin:	n/a	chr12:51663487-51663505 chr12:51663489-51663510 chr12:51663490-51663499
41	CTCF	chr12:51663299-51663639	ECC-1	luminal epithelium:	n/a	chr12:51663487-51663505 chr12:51663489-51663510 chr12:51663490-51663499
42	ZNF143	chr12:51663155-51664091	H1-hESC	embryonic stem cell:	n/a	chr12:51664070-51664080 chr12:51664010-51664020
43	RAD21	chr12:51663322-51663694	HepG2	liver:	n/a	chr12:51663488-51663507 chr12:51663489-51663498
44	MAX	chr12:51663106-51665113	ECC-1	luminal epithelium:	n/a	n/a
45	UBTF	chr12:51663405-51664681	K562	blood:	n/a	n/a
46	YY1	chr12:51663379-51663739	HepG2	liver:	n/a	chr12:51663639-51663653
47	CTCF	chr12:51663373-51663618	H1-hESC	embryonic stem cell:	n/a	chr12:51663487-51663505 chr12:51663489-51663510 chr12:51663490-51663499
48	E2F4	chr12:51663343-51663655	MCF10A-Er-Src	breast:	n/a	n/a
49	YY1	chr12:51663332-51663806	K562	blood:	n/a	chr12:51663639-51663653
50	CEBPB	chr12:51663293-51663549	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:51565300..51568760-chr12:51661642..51664290,3	K562	blood:
2	chr12:51661913..51666807-chr12:51714627..51721165,8	MCF-7	breast:
3	chr12:51474899..51477450-chr12:51661996..51663687,2	K562	blood:
4	chr12:51440322..51443098-chr12:51662230..51665433,4	K562	blood:
5	chr12:51662477..51664063-chr12:51717292..51718857,2	MCF-7	breast:
6	chr12:51630916..51632969-chr12:51661911..51664202,4	MCF-7	breast:
7	chr12:51631526..51635212-chr12:51662486..51664929,4	MCF-7	breast:
8	chr12:51397939..51400659-chr12:51662476..51664122,2	MCF-7	breast:
9	chr12:51661897..51665217-chr12:51739188..51742261,4	MCF-7	breast:
10	chr12:51663201..51663777-chr6:26158272..26158847,2	HCT-116	colon:

Variant related genes	Relation type
SMAGP	TF binding region
ENSG00000135457	Chromatin interaction
ENSG00000110934	Chromatin interaction
ENSG00000139610	Chromatin interaction
ENSG00000158373	Chromatin interaction
ENSG00000050426	Chromatin interaction
ENSG00000183283	Chromatin interaction
ENSG00000110911	Chromatin interaction
ENSG00000110925	Chromatin interaction

Extended variants
information (count: 3 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34039	chr12:51326702-51671911	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
2	nsv482304	chr12:51653496-51814917	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	esv3405622	chr12:51662910-51665458	Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51661000-51665000	Active TSS	Colonic Mucosa	Colon
2	chr12:51661400-51664800	Active TSS	Esophagus	oesophagus
3	chr12:51661600-51664600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr12:51661800-51664400	Active TSS	Rectal Mucosa Donor 29	rectum
5	chr12:51662600-51663600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr12:51662600-51663600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr12:51662600-51663600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr12:51662600-51663600	Flanking Active TSS	K562	blood
9	chr12:51662600-51663600	Flanking Active TSS	NH-A	brain
10	chr12:51662600-51664600	Active TSS	Sigmoid Colon	Sigmoid Colon
11	chr12:51662800-51663600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr12:51662800-51663600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr12:51662800-51663600	Flanking Active TSS	Placenta	Placenta
14	chr12:51662800-51663600	Active TSS	Stomach Mucosa	stomach
15	chr12:51662800-51663600	Flanking Active TSS	HUVEC	blood vessel
16	chr12:51662800-51663800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr12:51662800-51663800	Flanking Active TSS	Dnd41	blood
18	chr12:51662800-51664600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr12:51662800-51664600	Active TSS	Gastric	stomach
20	chr12:51662800-51664800	Active TSS	H9 Cell Line	embryonic stem cell
21	chr12:51662800-51664800	Bivalent/Poised TSS	Fetal Stomach	stomach
22	chr12:51662800-51664800	Active TSS	Ovary	ovary
23	chr12:51662800-51665000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
24	chr12:51662800-51665000	Active TSS	Left Ventricle	heart
25	chr12:51662800-51665000	Active TSS	Right Atrium	heart
26	chr12:51662800-51665000	Active TSS	Right Ventricle	heart
27	chr12:51662800-51665000	Active TSS	Small Intestine	intestine
28	chr12:51662800-51665400	Active TSS	Duodenum Smooth Muscle	Duodenum
29	chr12:51663000-51663600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
30	chr12:51663000-51663600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
31	chr12:51663000-51663600	Flanking Active TSS	Primary B cells from peripheral blood	blood
32	chr12:51663000-51663600	Flanking Active TSS	Primary hematopoietic stem cells	blood
33	chr12:51663000-51663600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
34	chr12:51663000-51663600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
35	chr12:51663000-51663600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
36	chr12:51663000-51663600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr12:51663000-51663600	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
38	chr12:51663000-51663600	Flanking Active TSS	HSMM	muscle
39	chr12:51663000-51663800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
40	chr12:51663000-51664200	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
41	chr12:51663000-51664400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
42	chr12:51663000-51664400	Bivalent/Poised TSS	Fetal Muscle Leg	muscle
43	chr12:51663000-51664600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
44	chr12:51663000-51664600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
45	chr12:51663000-51664600	Active TSS	Brain Anterior Caudate	brain
46	chr12:51663000-51664600	Active TSS	NHLF	lung
47	chr12:51663000-51664600	Active TSS	Osteobl	bone
48	chr12:51663000-51665000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr12:51663000-51665000	Flanking Active TSS	Primary B cells from cord blood	blood
50	chr12:51663000-51665200	Active TSS	Pancreatic Islets	Pancreatic Islet

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links