Variant report

Variant	rs74088160
Chromosome Location	chr12:49108969-49108970
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:49108836-49111405	IMR90	lung:	n/a	n/a
2	POLR2A	chr12:49108794-49109153	PFSK-1	brain:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:49103301..49108658-chr12:49108679..49112078,7	K562	blood:
2	chr12:49108930..49110553-chr12:49207843..49209517,2	MCF-7	breast:
3	chr12:49096349..49098245-chr12:49108578..49110236,2	K562	blood:
4	chr12:49072667..49077768-chr12:49107571..49112359,8	MCF-7	breast:
5	chr12:49108937..49110842-chr12:49180917..49183089,2	MCF-7	breast:
6	chr12:49108385..49110371-chr12:49210566..49212165,2	MCF-7	breast:
7	chr12:49073439..49079132-chr12:49108039..49112179,15	K562	blood:
8	chr12:49072639..49079132-chr12:49108469..49112073,12	K562	blood:
9	chr12:49072707..49077771-chr12:49103757..49111723,15	MCF-7	breast:

No data

Variant related genes	Relation type
CCNT1	TF binding region
ENSG00000129315	Chromatin interaction
ENSG00000257660	Chromatin interaction
ENSG00000139620	Chromatin interaction
ENSG00000167535	Chromatin interaction
ENSG00000174233	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs3902956	1.00[AFR][1000 genomes]
rs55823822	0.84[AFR][1000 genomes]
rs56015238	1.00[AFR][1000 genomes]
rs56037864	0.85[AFR][1000 genomes]
rs56306303	1.00[AFR][1000 genomes]
rs56942518	1.00[AFR][1000 genomes]
rs58685133	1.00[AFR][1000 genomes]
rs59636982	0.81[AFR][1000 genomes]
rs61522435	1.00[AFR][1000 genomes]
rs74088109	1.00[AFR][1000 genomes]
rs74088111	1.00[AFR][1000 genomes]
rs74088113	1.00[AFR][1000 genomes]
rs74088132	1.00[AFR][1000 genomes]
rs74088154	1.00[AFR][1000 genomes]
rs74088162	1.00[AFR][1000 genomes]
rs74089307	0.85[AFR][1000 genomes]
rs74089309	1.00[AFR][1000 genomes]
rs74089329	1.00[AFR][1000 genomes]
rs74089330	1.00[AFR][1000 genomes]
rs74089332	1.00[AFR][1000 genomes]
rs74089333	1.00[AFR][1000 genomes]
rs74089334	1.00[AFR][1000 genomes]
rs74089339	1.00[AFR][1000 genomes]
rs74089356	1.00[AFR][1000 genomes]
rs74089365	1.00[AFR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3332169	chr12:49005807-49150691	Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	43 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49076600-49109000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:49089800-49109400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr12:49097600-49109400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr12:49098200-49109600	Weak transcription	Aorta	Aorta
5	chr12:49099600-49109400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr12:49101000-49109000	Weak transcription	HSMMtube	muscle
7	chr12:49105400-49109400	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr12:49106400-49109000	Genic enhancers	Sigmoid Colon	Sigmoid Colon
9	chr12:49106400-49109400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
10	chr12:49106600-49109000	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
11	chr12:49107000-49109000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
12	chr12:49107200-49109000	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
13	chr12:49107200-49109200	Transcr. at gene 5' and 3'	Hela-S3	cervix
14	chr12:49107200-49109800	Enhancers	Small Intestine	intestine
15	chr12:49107200-49110400	Transcr. at gene 5' and 3'	Dnd41	blood
16	chr12:49107400-49109000	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr12:49107400-49109000	Genic enhancers	Left Ventricle	heart
18	chr12:49107400-49109000	Flanking Active TSS	HepG2	liver
19	chr12:49107600-49109000	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
20	chr12:49107600-49109200	Transcr. at gene 5' and 3'	A549	lung
21	chr12:49107600-49109400	Genic enhancers	Primary B cells from peripheral blood	blood
22	chr12:49107600-49109400	Genic enhancers	Fetal Thymus	thymus
23	chr12:49107600-49109600	Enhancers	Brain Angular Gyrus	brain
24	chr12:49107600-49109600	Enhancers	Stomach Mucosa	stomach
25	chr12:49107600-49109800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr12:49107800-49109000	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
27	chr12:49107800-49109000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
28	chr12:49107800-49109000	Genic enhancers	Cortex derived primary cultured neurospheres	brain
29	chr12:49107800-49109000	Enhancers	Fetal Kidney	kidney
30	chr12:49107800-49109000	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr12:49107800-49109000	Transcr. at gene 5' and 3'	NHEK	skin
32	chr12:49107800-49109200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr12:49107800-49109600	Enhancers	Fetal Heart	heart
34	chr12:49108000-49109000	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
35	chr12:49108000-49109000	Genic enhancers	Brain Anterior Caudate	brain
36	chr12:49108000-49109200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr12:49108000-49109400	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr12:49108000-49109400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr12:49108000-49109600	Enhancers	Thymus	Thymus
40	chr12:49108200-49109000	Enhancers	iPS-15b Cell Line	embryonic stem cell
41	chr12:49108200-49109000	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr12:49108200-49109000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr12:49108200-49109000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr12:49108200-49109200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr12:49108200-49109200	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr12:49108200-49109200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
47	chr12:49108200-49109400	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr12:49108200-49111600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr12:49108400-49109000	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr12:49108400-49109000	Genic enhancers	Primary hematopoietic stem cells	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links