Variant report

Variant	rs562629294
Chromosome Location	chr12:120805110-120805111
allele	A/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	CTCF	chr12:120805060-120805210	HUVEC	blood vessel:	n/a	chr12:120805126-120805139 chr12:120805124-120805142
2	CTCF	chr12:120805080-120805230	A549	lung:	n/a	chr12:120805126-120805139 chr12:120805124-120805142
3	CTCF	chr12:120805080-120805230	GM12872	blood:	n/a	chr12:120805126-120805139 chr12:120805124-120805142
4	CTCF	chr12:120805060-120805210	HVMF	connective:	n/a	chr12:120805126-120805139 chr12:120805124-120805142
5	CTCF	chr12:120805000-120805150	HAc	cerebellar:	n/a	chr12:120805126-120805139 chr12:120805124-120805142
6	CTCF	chr12:120805020-120805170	BE2_C	brain:	n/a	chr12:120805126-120805139 chr12:120805124-120805142
7	CTCF	chr12:120805049-120805223	NHEK	skin:	n/a	chr12:120805126-120805139 chr12:120805124-120805142
8	POLR2A	chr12:120805050-120806131	H1-hESC	embryonic stem cell:	n/a	n/a
9	ZNF143	chr12:120805020-120805254	K562	blood:	n/a	chr12:120805123-120805133
10	CTCF	chr12:120804972-120805300	K562	blood:	n/a	chr12:120805126-120805139 chr12:120805124-120805142
11	CTCF	chr12:120805032-120805222	MCF-7	breast:	n/a	chr12:120805126-120805139 chr12:120805124-120805142
12	E2F6	chr12:120805056-120805174	K562	blood:	n/a	n/a
13	CTCF	chr12:120805060-120805210	GM12875	blood:	n/a	chr12:120805126-120805139 chr12:120805124-120805142
14	CTCF	chr12:120805060-120805210	HCM	heart:	n/a	chr12:120805126-120805139 chr12:120805124-120805142
15	CTCF	chr12:120805036-120805186	Fibrobl	skin:	n/a	chr12:120805126-120805139 chr12:120805124-120805142
16	CTCF	chr12:120805100-120805250	HL-60	blood:	n/a	chr12:120805126-120805139 chr12:120805124-120805142
17	CTCF	chr12:120805080-120805230	HMF	breast:	n/a	chr12:120805126-120805139 chr12:120805124-120805142
18	CTCF	chr12:120805054-120805183	MCF-7	breast:	n/a	chr12:120805126-120805139 chr12:120805124-120805142
19	CTCF	chr12:120805060-120805210	HA-sp	spinal cord:	n/a	chr12:120805126-120805139 chr12:120805124-120805142
20	CTCF	chr12:120804929-120805222	K562	blood:	n/a	chr12:120805126-120805139 chr12:120805124-120805142
21	CTCF	chr12:120805081-120805254	GM20000	blood:	n/a	chr12:120805126-120805139 chr12:120805124-120805142
22	KAP1	chr12:120804916-120805551	U2OS	brain:	n/a	n/a
23	CTCF	chr12:120805060-120805210	AG10803	skin:	n/a	chr12:120805126-120805139 chr12:120805124-120805142
24	CTCF	chr12:120805040-120805190	HepG2	liver:	n/a	chr12:120805126-120805139 chr12:120805124-120805142
25	CTCF	chr12:120805015-120805248	GM19240	blood:	n/a	chr12:120805126-120805139 chr12:120805124-120805142
26	CTCF	chr12:120805080-120805230	GM12873	blood:	n/a	chr12:120805126-120805139 chr12:120805124-120805142
27	MAX	chr12:120804853-120805303	K562	blood:	n/a	n/a
28	SIN3A	chr12:120804888-120806061	H1-hESC	embryonic stem cell:	n/a	chr12:120805153-120805161
29	POLR2A	chr12:120804891-120806315	H1-hESC	embryonic stem cell:	n/a	n/a
30	CTCF	chr12:120805040-120805190	GM12870	blood:	n/a	chr12:120805126-120805139 chr12:120805124-120805142
31	CTCF	chr12:120805100-120805250	GM12864	blood:	n/a	chr12:120805126-120805139 chr12:120805124-120805142
32	CTCF	chr12:120805040-120805190	SAEC	small airway:	n/a	chr12:120805126-120805139 chr12:120805124-120805142
33	CTCF	chr12:120805047-120805240	HUVEC	blood vessel:	n/a	chr12:120805126-120805139 chr12:120805124-120805142
34	CTCF	chr12:120804980-120805130	GM06990	blood:	n/a	n/a
35	CTCF	chr12:120805020-120805247	MCF-7	breast:	n/a	chr12:120805126-120805139 chr12:120805124-120805142
36	CTCF	chr12:120805060-120805210	AG09319	gingival:	n/a	chr12:120805126-120805139 chr12:120805124-120805142
37	SMC3	chr12:120805078-120805233	HepG2	liver:	n/a	chr12:120805126-120805136 chr12:120805126-120805140
38	CTCF	chr12:120804835-120805257	K562	blood:	n/a	chr12:120805126-120805139 chr12:120805124-120805142
39	CTCF	chr12:120805060-120805210	BE2_C	brain:	n/a	chr12:120805126-120805139 chr12:120805124-120805142
40	CTCF	chr12:120805080-120805230	HPAF	blood vessel:	n/a	chr12:120805126-120805139 chr12:120805124-120805142
41	CTCF	chr12:120805042-120805219	GM13977	blood:	n/a	chr12:120805126-120805139 chr12:120805124-120805142
42	CTCF	chr12:120805020-120805170	GM12867	blood:	n/a	chr12:120805126-120805139 chr12:120805124-120805142
43	CTCF	chr12:120805063-120805208	A549	lung:	n/a	chr12:120805126-120805139 chr12:120805124-120805142
44	CTCF	chr12:120805040-120805190	WERI-Rb-1	eye:	n/a	chr12:120805126-120805139 chr12:120805124-120805142
45	CTCF	chr12:120805080-120805230	HPF	lung:	n/a	chr12:120805126-120805139 chr12:120805124-120805142
46	CTCF	chr12:120805040-120805190	AG04450	lung:	n/a	chr12:120805126-120805139 chr12:120805124-120805142
47	CTCF	chr12:120804980-120805236	GM12891	blood:	n/a	chr12:120805126-120805139 chr12:120805124-120805142
48	CTCF	chr12:120805020-120805170	HCFaa	heart:	n/a	chr12:120805126-120805139 chr12:120805124-120805142
49	CTCF	chr12:120805040-120805190	NHEK	skin:	n/a	chr12:120805126-120805139 chr12:120805124-120805142
50	CTCF	chr12:120805040-120805190	HFF-Myc	foreskin:	n/a	chr12:120805126-120805139 chr12:120805124-120805142

No.	Distal block	Cell Line	Cell type
1	chr12:120795985..120796800-chr12:120804726..120805531,3	MCF-7	breast:
2	chr12:120804639..120805497-chr12:120877167..120877760,2	MCF-7	breast:
3	chr12:120727901..120731375-chr12:120804063..120807248,3	K562	blood:
4	chr12:120803522..120805721-chr12:120933234..120935368,2	MCF-7	breast:
5	chr12:120794069..120794978-chr12:120804760..120805597,2	MCF-7	breast:
6	chr12:120803547..120806395-chr12:120907093..120909089,2	MCF-7	breast:

Variant related genes	Relation type
RPS27P25	TF binding region
ENSG00000202538	Chromatin interaction
ENSG00000088986	Chromatin interaction
ENSG00000248008	Chromatin interaction
ENSG00000111786	Chromatin interaction
ENSG00000200795	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	nsv899555	chr12:120519124-120840522	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	499 gene(s)	inside rSNPs	diseases
2	nsv1047447	chr12:120645330-120808621	Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	436 gene(s)	inside rSNPs	diseases
3	esv14211	chr12:120801254-120809932	Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv560437	chr12:120803783-120809590	Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:120800200-120805200	Genic enhancers	Fetal Intestine Small	intestine
2	chr12:120800200-120805400	Weak transcription	Ovary	ovary
3	chr12:120800400-120805600	Weak transcription	Right Atrium	heart
4	chr12:120802200-120805200	Enhancers	Stomach Mucosa	stomach
5	chr12:120802400-120805800	Enhancers	Sigmoid Colon	Sigmoid Colon
6	chr12:120803000-120805600	Enhancers	Pancreas	Pancrea
7	chr12:120803200-120805600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
8	chr12:120803400-120805200	Enhancers	Brain Anterior Caudate	brain
9	chr12:120803400-120805400	Genic enhancers	Fetal Stomach	stomach
10	chr12:120803400-120806000	Transcr. at gene 5' and 3'	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr12:120803600-120805400	Enhancers	Brain Inferior Temporal Lobe	brain
12	chr12:120803600-120805400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
13	chr12:120803600-120805600	Enhancers	Brain Cingulate Gyrus	brain
14	chr12:120803600-120806000	Enhancers	Fetal Brain Male	brain
15	chr12:120803600-120806200	Weak transcription	Lung	lung
16	chr12:120804000-120805200	Enhancers	Cortex derived primary cultured neurospheres	brain
17	chr12:120804000-120805200	Weak transcription	Fetal Kidney	kidney
18	chr12:120804000-120805800	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr12:120804000-120805800	Flanking Active TSS	Brain Germinal Matrix	brain
20	chr12:120804000-120806000	Enhancers	Rectal Mucosa Donor 31	rectum
21	chr12:120804000-120806000	Enhancers	A549	lung
22	chr12:120804200-120805200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr12:120804200-120805200	Enhancers	Rectal Mucosa Donor 29	rectum
24	chr12:120804200-120805400	Enhancers	Left Ventricle	heart
25	chr12:120804400-120805600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr12:120804400-120805800	Flanking Active TSS	Fetal Brain Female	brain
27	chr12:120804400-120805800	Enhancers	Fetal Heart	heart
28	chr12:120804400-120805800	Enhancers	Gastric	stomach
29	chr12:120804400-120806000	Enhancers	Brain Substantia Nigra	brain
30	chr12:120804400-120806200	Weak transcription	Liver	Liver
31	chr12:120804600-120805200	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
32	chr12:120804600-120805200	Enhancers	H9 Cell Line	embryonic stem cell
33	chr12:120804600-120805600	Enhancers	Right Ventricle	heart
34	chr12:120804600-120805800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr12:120804800-120805200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
36	chr12:120804800-120805200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr12:120804800-120805200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr12:120804800-120805200	Active TSS	iPS-15b Cell Line	embryonic stem cell
39	chr12:120804800-120805200	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr12:120804800-120805200	Bivalent Enhancer	Fetal Muscle Leg	muscle
41	chr12:120804800-120805400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
42	chr12:120804800-120805400	Bivalent Enhancer	NH-A	brain
43	chr12:120804800-120805600	Flanking Active TSS	Brain Hippocampus Middle	brain
44	chr12:120804800-120805600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
45	chr12:120804800-120805600	Bivalent Enhancer	Stomach Smooth Muscle	stomach
46	chr12:120804800-120805800	Bivalent Enhancer	HepG2	liver
47	chr12:120804800-120806000	Flanking Active TSS	H1 Cell Line	embryonic stem cell
48	chr12:120804800-120807800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr12:120804800-120807800	Active TSS	Pancreatic Islets	Pancreatic Islet
50	chr12:120805000-120805200	Bivalent Enhancer	Fetal Intestine Large	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links