Variant report

Variant	rs7688738
Chromosome Location	chr4:124426163-124426164
allele	G/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	RAD21	chr4:124426120-124427330	HepG2	liver:	n/a	n/a
2	TCF7L2	chr4:124426121-124427214	PANC-1	pancreas:	n/a	n/a
3	MAZ	chr4:124426065-124427146	HepG2	liver:	n/a	n/a
4	POLR2A	chr4:124426122-124426792	PANC-1	pancreas:	n/a	n/a
5	MBD4	chr4:124426059-124427315	HepG2	liver:	n/a	n/a
6	FOXA1	chr4:124426117-124427290	HepG2	liver:	n/a	chr4:124427005-124427017
7	RAD21	chr4:124426116-124427260	HepG2	liver:	n/a	n/a
8	FOXA2	chr4:124425729-124427592	HepG2	liver:	n/a	chr4:124427005-124427017
9	TEAD4	chr4:124425915-124427256	HepG2	liver:	n/a	n/a
10	HEY1	chr4:124426139-124427378	HepG2	liver:	n/a	chr4:124426805-124426820 chr4:124426790-124426805
11	HDAC2	chr4:124426131-124427223	HepG2	liver:	n/a	n/a
12	EP300	chr4:124426163-124427284	HepG2	liver:	n/a	chr4:124426312-124426322 chr4:124426801-124426810 chr4:124426798-124426807 chr4:124426804-124426813
13	MAX	chr4:124426112-124427508	HepG2	liver:	n/a	n/a
14	EP300	chr4:124426046-124427285	HepG2	liver:	n/a	chr4:124426312-124426322 chr4:124426801-124426810 chr4:124426798-124426807 chr4:124426804-124426813
15	NFIC	chr4:124426046-124427380	HepG2	liver:	n/a	n/a
16	MYBL2	chr4:124426068-124427403	HepG2	liver:	n/a	n/a
17	SP1	chr4:124426128-124427322	HepG2	liver:	n/a	chr4:124426364-124426374 chr4:124427099-124427113
18	CHD2	chr4:124426143-124427267	HepG2	liver:	n/a	chr4:124427045-124427055
19	SMC3	chr4:124426143-124427429	HepG2	liver:	n/a	n/a
20	FOXA1	chr4:124426052-124427276	HepG2	liver:	n/a	chr4:124427005-124427017
21	FOXA1	chr4:124426029-124427295	HepG2	liver:	n/a	chr4:124427005-124427017

Variant related genes	Relation type
ENSG00000251526	TF binding region

Extended variants
information (count: 10 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs13129216	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13129233	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1947372	0.93[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];0.95[ASN][1000 genomes]
rs2218977	0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6534408	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7655843	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9998488	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[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	nsv1006945	chr4:124206328-124503863	Enhancers Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv537240	chr4:124206328-124503863	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	esv34581	chr4:124271321-125247395	Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7688738	VSX1	trans	cerebellum	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:124417200-124426800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr4:124422400-124426600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr4:124423400-124426200	Weak transcription	HUVEC	blood vessel
4	chr4:124424400-124426200	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr4:124425000-124426200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr4:124425200-124426200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr4:124425200-124426200	Enhancers	Fetal Intestine Small	intestine
8	chr4:124425200-124426200	Enhancers	Fetal Kidney	kidney
9	chr4:124425200-124426200	Enhancers	Skeletal Muscle Male	skeletal muscle
10	chr4:124425200-124426800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr4:124425400-124426200	Enhancers	H1 Cell Line	embryonic stem cell
12	chr4:124425400-124426200	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr4:124425400-124426200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
14	chr4:124425400-124426200	Enhancers	Stomach Mucosa	stomach
15	chr4:124425600-124426200	Enhancers	Brain Hippocampus Middle	brain
16	chr4:124425600-124426200	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr4:124425600-124426400	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr4:124425600-124426400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr4:124425600-124426400	Weak transcription	Psoas Muscle	Psoas
20	chr4:124425600-124426600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr4:124425600-124427200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr4:124425800-124426200	Enhancers	HUES64 Cell Line	embryonic stem cell
23	chr4:124425800-124426200	Enhancers	iPS-15b Cell Line	embryonic stem cell
24	chr4:124425800-124426200	Enhancers	iPS-20b Cell Line	embryonic stem cell
25	chr4:124425800-124426600	Weak transcription	Gastric	stomach
26	chr4:124426000-124426200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr4:124426000-124426200	Active TSS	iPS-18 Cell Line	embryonic stem cell
28	chr4:124426000-124426200	Enhancers	Primary B cells from cord blood	blood
29	chr4:124426000-124426200	Enhancers	Primary T cells from cord blood	blood
30	chr4:124426000-124426200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr4:124426000-124426200	Enhancers	Adipose Nuclei	Adipose
32	chr4:124426000-124426200	Enhancers	Liver	Liver
33	chr4:124426000-124426200	Enhancers	Duodenum Mucosa	Duodenum
34	chr4:124426000-124426200	Enhancers	Fetal Brain Female	brain
35	chr4:124426000-124426200	Weak transcription	Fetal Intestine Large	intestine
36	chr4:124426000-124426200	Enhancers	Fetal Thymus	thymus
37	chr4:124426000-124426200	Enhancers	Rectal Mucosa Donor 31	rectum
38	chr4:124426000-124426400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr4:124426000-124426400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
40	chr4:124426000-124426400	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
41	chr4:124426000-124426600	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr4:124426000-124426600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
43	chr4:124426000-124427000	Active TSS	HepG2	liver
44	chr4:124426000-124427200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr4:124426000-124427600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr4:124426000-124427600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr4:124426000-124427600	Active TSS	Pancreatic Islets	Pancreatic Islet

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