Variant report

Variant	rs62109426
Chromosome Location	chr2:20213439-20213440
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TEAD4	chr2:20212283-20213452	HepG2	liver:	n/a	n/a
2	CTCF	chr2:20213320-20213470	GM06990	blood:	n/a	n/a
3	MYBL2	chr2:20212461-20213641	HepG2	liver:	n/a	n/a
4	MAX	chr2:20211720-20213557	HepG2	liver:	n/a	n/a
5	MBD4	chr2:20212918-20213624	HepG2	liver:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr2:20188544..20190994-chr2:20211302..20213941,2	MCF-7	breast:
2	chr2:20212605..20214922-chr2:20216980..20220655,3	MCF-7	breast:
3	chr2:20212620..20214988-chr2:20250395..20252051,2	MCF-7	breast:
4	chr2:20196234..20199275-chr2:20211073..20214096,3	MCF-7	breast:
5	chr2:20213367..20215755-chr2:20296083..20298973,4	MCF-7	breast:
6	chr2:20213361..20215470-chr2:20241959..20243915,2	MCF-7	breast:
7	chr2:20187710..20189541-chr2:20212607..20214933,2	K562	blood:
8	chr2:20208645..20229804-chr2:20247969..20254330,37	MCF-7	breast:
9	chr2:20187189..20189541-chr2:20212582..20214933,2	K562	blood:

No data

Variant related genes	Relation type
MATN3	TF binding region
ENSG00000227210	Chromatin interaction
ENSG00000068697	Chromatin interaction
ENSG00000223734	Chromatin interaction
ENSG00000132031	Chromatin interaction
ENSG00000118965	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10495701	1.00[AFR][1000 genomes]
rs11096632	1.00[AFR][1000 genomes]
rs11888045	1.00[AFR][1000 genomes]
rs11889206	1.00[AFR][1000 genomes]
rs12620863	1.00[AFR][1000 genomes]
rs1381817	1.00[AFR][1000 genomes]
rs62109398	1.00[AFR][1000 genomes]
rs62109413	1.00[AFR][1000 genomes]
rs62109415	1.00[AFR][1000 genomes]
rs62109420	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006404	chr2:20167688-20216509	Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv1011244	chr2:20174676-20216204	Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	esv3327327	chr2:20211296-20213844	Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
4	esv3393710	chr2:20211621-20213469	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs62109426	TTC32	Cis_1M	lymphoblastoid	RTeQTL
rs62109426	TTC32	cis	Esophagus Muscularis	GTEx
rs62109426	TTC32	cis	multi-tissue	Pritchard
rs62109426	TTC32	cis	Adipose Subcutaneous	GTEx
rs62109426	TTC32	cis	Heart Left Ventricle	GTEx

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20212600-20213600	Flanking Active TSS	HepG2	liver
2	chr2:20212800-20213600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:20212800-20213600	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
4	chr2:20212800-20216200	Weak transcription	HMEC	breast
5	chr2:20213000-20213600	Flanking Bivalent TSS/Enh	ES-I3 Cell Line	embryonic stem cell
6	chr2:20213000-20213600	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
7	chr2:20213000-20213600	Enhancers	Fetal Lung	lung
8	chr2:20213000-20213800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr2:20213000-20216200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr2:20213000-20218400	Weak transcription	Colon Smooth Muscle	Colon
11	chr2:20213000-20220600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr2:20213000-20227200	Weak transcription	Ovary	ovary
13	chr2:20213200-20213600	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
14	chr2:20213200-20213600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr2:20213200-20213600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr2:20213200-20217000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr2:20213200-20218400	Weak transcription	Fetal Heart	heart
18	chr2:20213200-20225000	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr2:20213200-20227000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr2:20213200-20227000	Weak transcription	Aorta	Aorta
21	chr2:20213400-20213600	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
22	chr2:20213400-20213600	Enhancers	H9 Cell Line	embryonic stem cell
23	chr2:20213400-20213600	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr2:20213400-20213600	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr2:20213400-20213600	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr2:20213400-20213600	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
27	chr2:20213400-20213600	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
28	chr2:20213400-20213600	Bivalent Enhancer	Primary hematopoietic stem cells	blood
29	chr2:20213400-20213600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr2:20213400-20214000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr2:20213400-20227400	Weak transcription	Fetal Kidney	kidney
32	chr2:20213400-20232200	Weak transcription	Right Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links