Variant report

Variant	rs12470971
Chromosome Location	chr2:11725241-11725242
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	POLR2A	chr2:11724815-11725670	HepG2	liver:	n/a	n/a
2	POLR2A	chr2:11725221-11726172	HepG2	liver:	n/a	n/a
3	POLR2A	chr2:11712005-11732311	MCF-7	breast:	n/a	n/a
4	POLR2A	chr2:11725017-11728081	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
GREB1	TF binding region

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11674184	0.87[CHB][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11679605	0.94[CEU][hapmap]
rs11679686	0.91[CHB][hapmap];0.89[CHD][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs11686429	0.83[ASN][1000 genomes]
rs12468019	0.87[ASN][1000 genomes]
rs12993278	0.95[ASN][1000 genomes]
rs13016186	0.94[ASN][1000 genomes]
rs13017593	0.97[ASN][1000 genomes]
rs13394619	0.83[CHD][hapmap]
rs16857668	1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17529680	0.95[CEU][hapmap]
rs1865573	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2358039	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2358040	0.91[CHB][hapmap];0.89[CHD][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs28689909	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2884374	0.91[CHB][hapmap];0.89[CHD][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs4669753	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4669754	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57439315	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59129126	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6746291	0.99[ASN][1000 genomes]
rs746579	0.83[CEU][hapmap]
rs9287734	0.81[CHB][hapmap]
rs9678410	0.85[ASN][1000 genomes]
rs9789525	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9798272	0.97[ASN][1000 genomes]

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	nsv1010506	chr2:11430965-12057286	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
2	nsv535585	chr2:11430965-12057286	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	nsv873663	chr2:11664349-11783775	Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11678400-11757000	Weak transcription	Right Ventricle	heart
2	chr2:11694800-11755200	Weak transcription	Gastric	stomach
3	chr2:11700000-11767000	Weak transcription	Right Atrium	heart
4	chr2:11711600-11738600	Weak transcription	Left Ventricle	heart
5	chr2:11714400-11765000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr2:11717600-11767000	Weak transcription	Fetal Intestine Small	intestine
7	chr2:11719200-11725800	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr2:11719200-11738000	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr2:11719400-11750800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr2:11720000-11735600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr2:11721600-11733000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:11721800-11726000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr2:11722000-11725600	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr2:11723000-11725400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr2:11723000-11740400	Weak transcription	Liver	Liver
16	chr2:11723200-11735400	Weak transcription	Brain Substantia Nigra	brain
17	chr2:11723400-11725800	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr2:11723400-11735200	Weak transcription	Fetal Lung	lung
19	chr2:11723400-11740000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr2:11723600-11735200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr2:11723600-11735600	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr2:11723600-11738600	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr2:11724200-11725400	Weak transcription	Ovary	ovary
24	chr2:11724200-11732800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr2:11724200-11732800	Weak transcription	Pancreas	Pancrea
26	chr2:11724400-11725400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr2:11724400-11725800	Weak transcription	Fetal Stomach	stomach
28	chr2:11724400-11735200	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr2:11724400-11735200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr2:11724400-11738000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr2:11724400-11738600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr2:11724400-11788600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
33	chr2:11724600-11725800	Weak transcription	Fetal Muscle Leg	muscle
34	chr2:11724600-11732800	Strong transcription	HepG2	liver
35	chr2:11724600-11735400	Weak transcription	Brain Hippocampus Middle	brain
36	chr2:11724600-11741000	Weak transcription	Brain Anterior Caudate	brain
37	chr2:11724600-11766800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr2:11724600-11766800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr2:11724800-11727200	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr2:11724800-11735400	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr2:11724800-11735600	Weak transcription	Brain Angular Gyrus	brain
42	chr2:11724800-11736000	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr2:11724800-11749600	Weak transcription	Brain Cingulate Gyrus	brain
44	chr2:11725000-11743800	Weak transcription	Fetal Kidney	kidney
45	chr2:11725200-11725400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr2:11725200-11725600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr2:11725200-11730200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr2:11725200-11730600	Strong transcription	Fetal Muscle Trunk	muscle

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