Variant report

Variant	rs11051472
Chromosome Location	chr12:31739162-31739163
allele	C/T
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	chr12:31737848-31743421	HepG2	liver:	n/a	n/a
2	STAT3	chr12:31739078-31739278	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:31733774..31735738-chr12:31738884..31740641,2	K562	blood:
2	chr12:31733749..31740034-chr12:31741014..31744449,13	K562	blood:
3	chr12:31737999..31740924-chr12:31746512..31749363,2	K562	blood:
4	chr12:31730582..31735738-chr12:31737602..31740641,5	K562	blood:

Variant related genes	Relation type
DENND5B-AS1	TF binding region
ENSG00000252390	Chromatin interaction
ENSG00000170456	Chromatin interaction
ENSG00000255867	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10771830	0.82[EUR][1000 genomes]
rs10771833	0.84[EUR][1000 genomes]
rs10771835	0.85[EUR][1000 genomes]
rs10771837	0.84[EUR][1000 genomes]
rs10843953	0.85[EUR][1000 genomes]
rs10843954	0.84[EUR][1000 genomes]
rs10843957	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10843962	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10843966	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10843968	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10843969	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10843971	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10843972	0.90[EUR][1000 genomes]
rs11051428	0.81[EUR][1000 genomes]
rs11051440	0.88[EUR][1000 genomes]
rs11051446	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11051454	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11051461	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11051467	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11051476	0.91[EUR][1000 genomes]
rs11051478	0.83[EUR][1000 genomes]
rs1150949	0.84[ASN][1000 genomes]
rs12368987	0.91[EUR][1000 genomes]
rs12369701	0.88[ASN][1000 genomes]
rs12371432	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1259360	0.84[ASN][1000 genomes]
rs1268747	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1677193	0.87[ASN][1000 genomes]
rs16918740	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1879385	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2163730	0.80[EUR][1000 genomes]
rs2351921	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2351922	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2351923	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34498192	0.83[EUR][1000 genomes]
rs3741878	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3803114	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3850966	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3887250	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3898712	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4930979	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4931499	0.83[EUR][1000 genomes]
rs4931511	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4931512	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4931513	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61097018	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6487991	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6487995	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7132688	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7136559	0.84[EUR][1000 genomes]
rs7297507	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7300106	0.81[EUR][1000 genomes]
rs7302695	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73080572	0.81[EUR][1000 genomes]
rs7308202	0.81[EUR][1000 genomes]
rs7311970	0.91[EUR][1000 genomes]
rs7960380	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7963764	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7980274	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041877	chr12:31009451-31809254	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription 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 target site	71 gene(s)	inside rSNPs	diseases
2	nsv541440	chr12:31009451-31809254	ZNF genes & repeats Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
3	esv1836923	chr12:31539122-31761172	Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	esv2760267	chr12:31626732-31909908	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
5	nsv898965	chr12:31631819-31771689	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv832365	chr12:31642811-31808532	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	esv1842653	chr12:31670378-31744033	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	esv1797962	chr12:31733044-31761172	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:31721600-31742400	Weak transcription	Aorta	Aorta
2	chr12:31726400-31742000	Weak transcription	Fetal Intestine Large	intestine
3	chr12:31728000-31741000	Weak transcription	Right Ventricle	heart
4	chr12:31728400-31741800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr12:31732000-31741400	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr12:31732200-31741600	Weak transcription	Fetal Kidney	kidney
7	chr12:31732400-31741000	Weak transcription	Pancreas	Pancrea
8	chr12:31735800-31739800	Weak transcription	Spleen	Spleen
9	chr12:31736800-31740000	Enhancers	Fetal Heart	heart
10	chr12:31737000-31739400	Enhancers	HSMMtube	muscle
11	chr12:31737400-31741000	Weak transcription	Brain Germinal Matrix	brain
12	chr12:31737800-31741800	Flanking Active TSS	GM12878-XiMat	blood
13	chr12:31738000-31739200	Enhancers	Liver	Liver
14	chr12:31738000-31740200	ZNF genes & repeats	Primary B cells from peripheral blood	blood
15	chr12:31738200-31739200	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr12:31738200-31739200	Flanking Active TSS	A549	lung
17	chr12:31738200-31739600	Enhancers	Primary B cells from cord blood	blood
18	chr12:31738400-31739800	Enhancers	Duodenum Mucosa	Duodenum
19	chr12:31738400-31742400	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr12:31738400-31742600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr12:31738400-31742600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr12:31738400-31742600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr12:31738400-31742600	Weak transcription	Lung	lung
24	chr12:31738600-31739600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr12:31738600-31741000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr12:31738600-31741000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr12:31738600-31741000	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr12:31738600-31741000	Weak transcription	Psoas Muscle	Psoas
29	chr12:31738600-31741200	Weak transcription	Fetal Brain Female	brain
30	chr12:31738600-31741600	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr12:31738600-31741600	Weak transcription	Fetal Muscle Leg	muscle
32	chr12:31738600-31741600	Weak transcription	HUVEC	blood vessel
33	chr12:31738600-31741800	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr12:31738600-31741800	Weak transcription	NHDF-Ad	bronchial
35	chr12:31738600-31742200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr12:31738600-31742400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr12:31738600-31742400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr12:31738600-31742600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr12:31738800-31739200	Enhancers	Skeletal Muscle Female	skeletal muscle
40	chr12:31738800-31739800	Enhancers	Fetal Intestine Small	intestine
41	chr12:31738800-31739800	Weak transcription	Ovary	ovary
42	chr12:31738800-31739800	Weak transcription	K562	blood
43	chr12:31738800-31741000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr12:31738800-31741000	Weak transcription	Brain Substantia Nigra	brain
45	chr12:31738800-31741000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr12:31738800-31741000	Weak transcription	Left Ventricle	heart
47	chr12:31738800-31741200	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr12:31738800-31741200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr12:31738800-31741200	Weak transcription	Brain Hippocampus Middle	brain
50	chr12:31738800-31741400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links