Variant report

Variant	rs11686597
Chromosome Location	chr2:62716781-62716782
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	TCF12	chr2:62716138-62716807	SK-N-SH	brain:	n/a	chr2:62716585-62716594
2	EP300	chr2:62716723-62717198	HepG2	liver:	n/a	n/a
3	FOXA1	chr2:62716774-62717162	HepG2	liver:	n/a	chr2:62717011-62717023
4	FOXA1	chr2:62716744-62717131	HepG2	liver:	n/a	chr2:62717011-62717023

Variant related genes	Relation type
RN7SL18P	TF binding region

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11678340	0.86[AMR][1000 genomes]
rs11690138	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12988497	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12989129	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12993270	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34264648	0.88[AMR][1000 genomes]
rs34282247	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36006708	0.86[AMR][1000 genomes]
rs4608498	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6545946	0.97[ASN][1000 genomes]
rs72805579	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72805589	0.86[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv535766	chr2:62177655-62929746	Bivalent/Poised TSS Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv916190	chr2:62233785-63006200	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv932487	chr2:62258290-63006200	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers 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 miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv535767	chr2:62461582-63413596	Bivalent Enhancer Strong transcription Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
5	nsv2751	chr2:62691264-62737131	Strong transcription Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:62703600-62724800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:62705800-62732200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr2:62706600-62726600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr2:62713400-62732400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr2:62714000-62718600	Weak transcription	Esophagus	oesophagus
6	chr2:62714000-62728000	Weak transcription	Brain Anterior Caudate	brain
7	chr2:62714200-62717200	Weak transcription	Fetal Muscle Trunk	muscle
8	chr2:62714200-62732400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr2:62714400-62728400	Weak transcription	HMEC	breast
10	chr2:62715200-62718000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr2:62715400-62717800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr2:62715800-62716800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr2:62715800-62717200	Enhancers	Osteobl	bone
14	chr2:62715800-62717400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr2:62716000-62716800	Enhancers	Fetal Lung	lung
16	chr2:62716000-62716800	Enhancers	Rectal Smooth Muscle	rectum
17	chr2:62716000-62716800	Enhancers	NHEK	skin
18	chr2:62716000-62717000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr2:62716000-62717200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr2:62716000-62717200	Enhancers	Fetal Stomach	stomach
21	chr2:62716000-62717600	Enhancers	Fetal Muscle Leg	muscle
22	chr2:62716200-62716800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr2:62716200-62716800	Enhancers	Adipose Nuclei	Adipose
24	chr2:62716200-62716800	Enhancers	Brain Cingulate Gyrus	brain
25	chr2:62716200-62716800	Enhancers	Brain Hippocampus Middle	brain
26	chr2:62716200-62720400	Enhancers	HepG2	liver
27	chr2:62716400-62716800	Enhancers	HSMMtube	muscle
28	chr2:62716400-62716800	Enhancers	NH-A	brain
29	chr2:62716400-62717000	Enhancers	A549	lung
30	chr2:62716400-62717200	Enhancers	Fetal Kidney	kidney
31	chr2:62716600-62716800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
32	chr2:62716600-62717000	Weak transcription	Ovary	ovary
33	chr2:62716600-62717200	Enhancers	NHDF-Ad	bronchial
34	chr2:62716600-62718200	Weak transcription	Liver	Liver
35	chr2:62716600-62719800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr2:62716600-62722200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr2:62716600-62723200	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr2:62716600-62728200	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr2:62716600-62732200	Weak transcription	Brain Angular Gyrus	brain
40	chr2:62716600-62732400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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