Variant report

Variant	rs3774428
Chromosome Location	chr3:53565829-53565830
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:21)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:21 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA1	chr3:53565827-53566001	T-47D	breast:	n/a	n/a
2	CTCF	chr3:53565800-53565950	GM12870	blood:	n/a	n/a
3	CTCF	chr3:53565707-53566151	MCF-7	breast:	n/a	n/a
4	RAD21	chr3:53565675-53566259	MCF-7	breast:	n/a	n/a
5	ZNF143	chr3:53565819-53566019	GM12878	blood:	n/a	n/a
6	SMC3	chr3:53565786-53566148	GM12878	blood:	n/a	n/a
7	CTCF	chr3:53565784-53566121	GM12878	blood:	n/a	n/a
8	CTCF	chr3:53565780-53565930	HCT-116	colon:	n/a	n/a
9	CTCF	chr3:53565800-53565950	GM12869	blood:	n/a	n/a
10	RAD21	chr3:53565811-53566226	MCF-7	breast:	n/a	n/a
11	SMC3	chr3:53565819-53566045	Hela-S3	cervix:	n/a	n/a
12	CTCF	chr3:53565823-53566035	T-47D	breast:	n/a	n/a
13	RAD21	chr3:53565829-53566157	ECC-1	luminal epithelium:	n/a	n/a
14	CTCF	chr3:53565800-53565950	HCT-116	colon:	n/a	n/a
15	CTCF	chr3:53565800-53565950	HEK293	kidney:	n/a	n/a
16	RAD21	chr3:53565688-53566212	HCT-116	colon:	n/a	n/a
17	CTCF	chr3:53565803-53566155	MCF-7	breast:	n/a	n/a
18	CTCF	chr3:53565827-53566009	HepG2	liver:	n/a	n/a
19	CTCF	chr3:53565827-53566065	MCF-7	breast:	n/a	n/a
20	CTCF	chr3:53565820-53565970	GM12875	blood:	n/a	n/a
21	CTCF	chr3:53565820-53565970	GM12868	blood:	n/a	n/a

No data

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

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

No data

Variant related genes	Relation type
ENSG00000251987	TF binding region

Extended variants
information (count: 22 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1074235	0.93[ASN][1000 genomes]
rs1547949	0.92[CHB][hapmap];0.90[JPT][hapmap];0.87[YRI][hapmap];0.94[ASN][1000 genomes]
rs17053168	0.82[CEU][hapmap];0.86[EUR][1000 genomes]
rs33999362	0.86[ASN][1000 genomes]
rs3774425	0.85[TSI][hapmap]
rs3774439	0.83[CEU][hapmap];0.90[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3774440	0.83[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3774441	0.86[EUR][1000 genomes]
rs3821847	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.84[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59422128	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59512909	0.81[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs62251864	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62251868	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62251869	0.93[ASN][1000 genomes]
rs62251870	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62251903	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62251904	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6764908	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72957281	0.96[AFR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs740756	1.00[CHB][hapmap];0.90[JPT][hapmap];0.97[ASN][1000 genomes]
rs9311502	1.00[CEU][hapmap];0.97[TSI][hapmap];0.96[EUR][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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3774428	DCP1A	cis	parietal	SCAN
rs3774428	RNF123	cis	parietal	SCAN
rs3774428	GNL3	cis	cerebellum	SCAN
rs3774428	SPCS1	cis	parietal	SCAN

Chromatin state (count:20 , 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	chr3:53563600-53566000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr3:53563600-53569400	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr3:53564800-53568600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr3:53564800-53579400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:53565400-53566600	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr3:53565600-53566400	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr3:53565600-53566400	Enhancers	Fetal Intestine Small	intestine
13	chr3:53565800-53566200	Enhancers	H9 Cell Line	embryonic stem cell
14	chr3:53565800-53566200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr3:53565800-53566400	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr3:53565800-53566400	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chr3:53565800-53566400	Enhancers	HUES64 Cell Line	embryonic stem cell
18	chr3:53565800-53566400	Genic enhancers	Fetal Intestine Large	intestine
19	chr3:53565800-53566800	Genic enhancers	Fetal Lung	lung
20	chr3:53565800-53567600	Enhancers	iPS-20b Cell Line	embryonic stem cell

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