Variant report

Variant	rs2239759
Chromosome Location	chr12:121162882-121162883
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:121162735-121162989	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr12:121162579-121164122	ECC-1	luminal epithelium:	n/a	n/a
3	POLR2A	chr12:121162269-121163936	Hela-S3	cervix:	n/a	n/a
4	MXI1	chr12:121162805-121164417	SK-N-SH	brain:	n/a	n/a
5	POLR2A	chr12:121162574-121162908	HepG2	liver:	n/a	n/a
6	POLR2A	chr12:121162863-121164065	SK-N-MC	brain:	n/a	n/a
7	POLR2A	chr12:121162800-121163010	HUVEC	blood vessel:	n/a	n/a
8	POLR2A	chr12:121162080-121163810	K562	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:121018631..121020878-chr12:121162530..121164769,2	MCF-7	breast:
2	chr12:121124457..121126009-chr12:121161896..121164295,2	K562	blood:
3	chr12:121136675..121138856-chr12:121162469..121164078,2	K562	blood:
4	chr12:121148319..121151196-chr12:121161623..121163655,2	K562	blood:
5	chr12:121146305..121152610-chr12:121160959..121168394,8	MCF-7	breast:
6	chr12:121124509..121126833-chr12:121162138..121164295,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000256569	TF binding region
ACADS	TF binding region
ENSG00000110917	Chromatin interaction
ENSG00000167272	Chromatin interaction
ENSG00000256364	Chromatin interaction
ENSG00000175970	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10431372	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10431383	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10849774	0.86[EUR][1000 genomes]
rs10849780	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10849781	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11065184	0.86[EUR][1000 genomes]
rs11065186	0.86[EUR][1000 genomes]
rs11065188	0.86[EUR][1000 genomes]
rs11065189	0.86[EUR][1000 genomes]
rs11065191	0.86[EUR][1000 genomes]
rs11065192	0.86[EUR][1000 genomes]
rs11065193	0.86[EUR][1000 genomes]
rs11065194	1.00[EUR][1000 genomes]
rs11065195	1.00[EUR][1000 genomes]
rs11065196	1.00[EUR][1000 genomes]
rs11065197	1.00[EUR][1000 genomes]
rs11065198	1.00[EUR][1000 genomes]
rs11065199	1.00[EUR][1000 genomes]
rs11065204	1.00[EUR][1000 genomes]
rs11065205	1.00[EUR][1000 genomes]
rs11065214	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11065215	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11065217	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11065220	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11065221	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11065224	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11065229	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11065234	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11065235	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11065238	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11065240	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11065241	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11065242	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11065243	0.91[ASN][1000 genomes]
rs11065244	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11065245	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11065246	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11065262	0.83[EUR][1000 genomes]
rs12228118	1.00[EUR][1000 genomes]
rs12228187	0.86[EUR][1000 genomes]
rs12229164	1.00[EUR][1000 genomes]
rs12229181	1.00[EUR][1000 genomes]
rs12231101	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12231499	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17848090	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2071266	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2229534	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2239687	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2239757	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3751166	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3809310	0.86[EUR][1000 genomes]
rs3809311	0.86[EUR][1000 genomes]
rs7302002	1.00[EUR][1000 genomes]
rs7973568	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]

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	nsv521928	chr12:121041728-121761800	Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv899557	chr12:121069201-121189116	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh 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 miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1037070	chr12:121069938-121459047	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv899558	chr12:121161589-121179939	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	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	chr12:121150000-121163000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr12:121150400-121163200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:121151000-121163000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr12:121151200-121163000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr12:121151400-121163600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr12:121157600-121163000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr12:121158200-121163000	Weak transcription	Stomach Mucosa	stomach
8	chr12:121158400-121163200	Weak transcription	Psoas Muscle	Psoas
9	chr12:121158400-121163600	Weak transcription	Small Intestine	intestine
10	chr12:121158600-121163000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr12:121160200-121163600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr12:121160600-121163000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr12:121161000-121163000	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr12:121161000-121163000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr12:121161000-121163000	Weak transcription	Colonic Mucosa	Colon
16	chr12:121161000-121163200	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr12:121161200-121163000	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr12:121161200-121163000	Weak transcription	Rectal Smooth Muscle	rectum
19	chr12:121161200-121163000	Weak transcription	Right Ventricle	heart
20	chr12:121161200-121163000	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr12:121161200-121163000	Weak transcription	GM12878-XiMat	blood
22	chr12:121161200-121163000	Weak transcription	HMEC	breast
23	chr12:121161200-121163200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr12:121161200-121163200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr12:121161200-121163200	Weak transcription	Esophagus	oesophagus
26	chr12:121161200-121163200	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr12:121161400-121163000	Weak transcription	Primary B cells from cord blood	blood
28	chr12:121161600-121163000	Weak transcription	Primary T cells from cord blood	blood
29	chr12:121161600-121163000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr12:121161600-121163000	Weak transcription	Brain Cingulate Gyrus	brain
31	chr12:121161600-121163000	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr12:121161800-121163000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr12:121161800-121163000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr12:121162400-121163000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr12:121162400-121163000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr12:121162400-121163000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr12:121162400-121163000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr12:121162600-121163000	Enhancers	H9 Cell Line	embryonic stem cell
39	chr12:121162600-121163000	Enhancers	HUES48 Cell Line	embryonic stem cell
40	chr12:121162600-121163000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr12:121162600-121163000	Enhancers	Breast Myoepithelial Primary Cells	Breast
42	chr12:121162600-121163000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr12:121162600-121163000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr12:121162600-121163000	Enhancers	Brain Anterior Caudate	brain
45	chr12:121162600-121163000	Enhancers	Brain Hippocampus Middle	brain
46	chr12:121162600-121163000	Enhancers	Brain Inferior Temporal Lobe	brain
47	chr12:121162600-121163000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
48	chr12:121162600-121163000	Enhancers	Colon Smooth Muscle	Colon
49	chr12:121162600-121163000	Enhancers	Duodenum Smooth Muscle	Duodenum
50	chr12:121162600-121163000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links