Variant report

Variant	rs3774429
Chromosome Location	chr3:53566406-53566407
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	CTCF	chr3:53566320-53566470	GM12873	blood:	n/a	n/a
2	CTCF	chr3:53566280-53566430	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:53565593..53566409-chr3:53702634..53703149,2	MCF-7	breast:
2	chr3:53565964..53566939-chr3:53744231..53744799,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000251987	TF binding region

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1002578	1.00[CHB][hapmap];0.88[JPT][hapmap];0.93[ASN][1000 genomes]
rs10440150	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1123895	1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs13323471	0.85[CHB][hapmap];0.95[ASN][1000 genomes]
rs17053146	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17053233	1.00[TSI][hapmap]
rs17053265	1.00[TSI][hapmap]
rs17053279	1.00[TSI][hapmap]
rs2109182	1.00[TSI][hapmap]
rs28620592	0.95[ASN][1000 genomes]
rs3774427	1.00[TSI][hapmap]
rs3774430	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs3774431	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs3774442	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[TSI][hapmap];0.98[ASN][1000 genomes]
rs3774443	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[TSI][hapmap];0.93[ASN][1000 genomes]
rs3774447	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[ASN][1000 genomes]
rs3821845	0.95[ASN][1000 genomes]
rs9311503	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9311504	1.00[CHB][hapmap];0.88[JPT][hapmap];0.93[ASN][1000 genomes]
rs979220	0.89[JPT][hapmap]
rs9821489	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[TSI][hapmap];0.98[ASN][1000 genomes]
rs9865394	0.95[ASN][1000 genomes]
rs9882823	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003621	chr3:53448934-54425322	Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53552400-53568400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr3:53560400-53566800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr3:53560400-53568400	Weak transcription	Pancreas	Pancrea
4	chr3:53560600-53587000	Weak transcription	Duodenum Mucosa	Duodenum
5	chr3:53561000-53568800	Weak transcription	Colon Smooth Muscle	Colon
6	chr3:53563600-53569400	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr3:53564800-53568600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr3:53564800-53579400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:53565400-53566600	Enhancers	HUES48 Cell Line	embryonic stem cell
10	chr3:53565800-53566800	Genic enhancers	Fetal Lung	lung
11	chr3:53565800-53567600	Enhancers	iPS-20b Cell Line	embryonic stem cell
12	chr3:53566000-53566600	Enhancers	H1 Cell Line	embryonic stem cell
13	chr3:53566000-53566600	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr3:53566000-53567000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr3:53566000-53567800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr3:53566200-53566600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr3:53566400-53566600	Enhancers	Aorta	Aorta
18	chr3:53566400-53566600	Enhancers	Fetal Brain Female	brain
19	chr3:53566400-53566800	Weak transcription	Fetal Intestine Small	intestine
20	chr3:53566400-53567200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr3:53566400-53569000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr3:53566400-53569600	Strong transcription	Fetal Intestine Large	intestine
23	chr3:53566400-53583200	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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