Variant report

Variant	rs28757753
Chromosome Location	chr12:121988642-121988643
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	FOXA2	chr12:121988475-121989602	HepG2	liver:	n/a	chr12:121989103-121989115
2	NR2F2	chr12:121988600-121989627	HepG2	liver:	n/a	n/a
3	NR2F2	chr12:121988590-121989354	HepG2	liver:	n/a	n/a
4	FOXA1	chr12:121988635-121989362	HepG2	liver:	n/a	chr12:121989103-121989115
5	TEAD4	chr12:121988555-121989416	HepG2	liver:	n/a	n/a
6	FOXA1	chr12:121988598-121989438	HepG2	liver:	n/a	chr12:121989103-121989115
7	MYBL2	chr12:121988591-121989422	HepG2	liver:	n/a	n/a
8	TCF7L2	chr12:121988587-121989441	HepG2	liver:	n/a	chr12:121989116-121989125

No.	Distal block	Cell Line	Cell type
1	chr12:121972742..121976523-chr12:121985100..121990052,4	K562	blood:
2	chr12:121987323..121991589-chr12:122015980..122018755,4	K562	blood:
3	chr12:121986936..121988892-chr12:122109089..122111571,2	MCF-7	breast:
4	chr12:121987896..121991589-chr12:122016532..122018755,3	K562	blood:
5	chr12:121985158..121989788-chr12:122063533..122067478,5	K562	blood:
6	chr12:121973342..121977941-chr12:121987524..121992877,7	MCF-7	breast:

Variant related genes	Relation type
KDM2B	TF binding region
ENSG00000182500	Chromatin interaction
ENSG00000089094	Chromatin interaction
ENSG00000139714	Chromatin interaction
ENSG00000256742	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs28373517	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28379971	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28397967	0.89[EUR][1000 genomes]
rs28451063	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28481788	0.88[EUR][1000 genomes]
rs28604990	0.82[EUR][1000 genomes]
rs28618294	0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs28620502	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28663167	0.81[EUR][1000 genomes]
rs28667673	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28671138	0.81[EUR][1000 genomes]
rs28687122	0.88[EUR][1000 genomes]
rs28728162	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28845610	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4981000	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4981004	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4981013	0.95[AMR][1000 genomes]
rs4981016	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053272	chr12:121956483-122132477	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
2	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121976400-121990000	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr12:121976400-122001200	Strong transcription	Dnd41	blood
3	chr12:121976600-121988800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr12:121976600-121989800	Weak transcription	HSMMtube	muscle
5	chr12:121976600-122006800	Weak transcription	Fetal Lung	lung
6	chr12:121976600-122014600	Weak transcription	Colonic Mucosa	Colon
7	chr12:121976800-121990600	Weak transcription	Colon Smooth Muscle	Colon
8	chr12:121976800-121995400	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr12:121976800-121998600	Weak transcription	NHDF-Ad	bronchial
10	chr12:121977000-121989400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr12:121977000-121990600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr12:121977200-121990800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr12:121977200-121990800	Weak transcription	Stomach Mucosa	stomach
14	chr12:121977200-122015200	Weak transcription	Small Intestine	intestine
15	chr12:121978000-121997000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr12:121978400-121990000	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr12:121978800-121990000	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr12:121979200-121990000	Strong transcription	H1 Cell Line	embryonic stem cell
19	chr12:121979200-121990400	Strong transcription	HUES48 Cell Line	embryonic stem cell
20	chr12:121979400-122006000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr12:121979600-121993000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
22	chr12:121979600-121993200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
23	chr12:121980200-121989800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr12:121981600-122000800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr12:121985200-121989800	Weak transcription	Primary B cells from peripheral blood	blood
26	chr12:121986000-122012000	Weak transcription	Primary hematopoietic stem cells	blood
27	chr12:121986200-121990400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr12:121986200-121997000	Weak transcription	Monocytes-CD14+_RO01746	blood
29	chr12:121986800-122006800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr12:121986800-122006800	Weak transcription	Rectal Smooth Muscle	rectum
31	chr12:121986800-122011800	Weak transcription	Brain Hippocampus Middle	brain
32	chr12:121987000-121998000	Weak transcription	Placenta	Placenta
33	chr12:121987000-122006800	Weak transcription	Right Ventricle	heart
34	chr12:121987200-121990800	Weak transcription	Stomach Smooth Muscle	stomach
35	chr12:121987200-121991400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr12:121987200-122006800	Weak transcription	NHLF	lung
37	chr12:121987200-122011800	Weak transcription	Fetal Intestine Large	intestine
38	chr12:121987400-121991400	Weak transcription	Lung	lung
39	chr12:121987400-121993600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr12:121987400-121994000	Weak transcription	Left Ventricle	heart
41	chr12:121987400-121997800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr12:121987400-121998600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr12:121987400-122007000	Weak transcription	Ovary	ovary
44	chr12:121987400-122011800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr12:121987400-122011800	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr12:121987600-121989800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr12:121987600-121990000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr12:121987600-121990400	Weak transcription	Esophagus	oesophagus
49	chr12:121987600-121990800	Weak transcription	Fetal Thymus	thymus
50	chr12:121987600-121990800	Weak transcription	Pancreas	Pancrea

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links