Variant report

Variant	rs55845468
Chromosome Location	chr3:196244495-196244496
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:32)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr3:196244325-196244643	GM12878	blood:	n/a	n/a
2	ARID3A	chr3:196244017-196244530	K562	blood:	n/a	n/a
3	TCF12	chr3:196244277-196245250	ECC-1	luminal epithelium:	n/a	n/a
4	CTCF	chr3:196244331-196244628	GM12878	blood:	n/a	n/a
5	CTCF	chr3:196244362-196244621	K562	blood:	n/a	n/a
6	CTCF	chr3:196244041-196244588	K562	blood:	n/a	n/a
7	CTCF	chr3:196244390-196244534	HepG2	liver:	n/a	n/a
8	CTCF	chr3:196244420-196244570	K562	blood:	n/a	n/a
9	CTCF	chr3:196244373-196244587	Hela-S3	cervix:	n/a	n/a
10	RAD21	chr3:196244215-196244779	HCT-116	colon:	n/a	n/a
11	CTCF	chr3:196244382-196244589	K562	blood:	n/a	n/a
12	RCOR1	chr3:196244121-196244555	K562	blood:	n/a	n/a
13	ZNF143	chr3:196244484-196244534	H1-hESC	embryonic stem cell:	n/a	n/a
14	JUND	chr3:196244130-196244549	K562	blood:	n/a	n/a
15	EP300	chr3:196244256-196244502	K562	blood:	n/a	n/a
16	MYC	chr3:196244117-196244529	K562	blood:	n/a	n/a
17	RAD21	chr3:196244200-196244956	Hela-S3	cervix:	n/a	n/a
18	CTCF	chr3:196244380-196244530	GM06990	blood:	n/a	n/a
19	CTCF	chr3:196244462-196244532	HepG2	liver:	n/a	n/a
20	CTCF	chr3:196244228-196244714	HCT-116	colon:	n/a	n/a
21	JUN	chr3:196243852-196246433	K562	blood:	n/a	chr3:196246149-196246162
22	POLR2A	chr3:196244221-196244537	ECC-1	luminal epithelium:	n/a	n/a
23	RAD21	chr3:196244352-196244551	GM12878	blood:	n/a	n/a
24	CTCF	chr3:196244428-196244515	GM12878	blood:	n/a	n/a
25	RAD21	chr3:196244329-196244535	K562	blood:	n/a	n/a
26	CTCF	chr3:196244022-196244664	K562	blood:	n/a	n/a
27	MAZ	chr3:196244131-196244600	K562	blood:	n/a	n/a
28	CTCF	chr3:196244112-196244553	K562	blood:	n/a	n/a
29	SMC3	chr3:196244229-196244621	Hela-S3	cervix:	n/a	n/a
30	RAD21	chr3:196244393-196244529	K562	blood:	n/a	n/a
31	SMC3	chr3:196244196-196244572	K562	blood:	n/a	n/a
32	RAD21	chr3:196244199-196244753	HCT-116	colon:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:196200904..196203106-chr3:196242169..196245085,2	K562	blood:
2	chr3:195808137..195810508-chr3:196244076..196245932,2	K562	blood:

No data

Variant related genes	Relation type
SMCO1	TF binding region
ENSG00000072274	Chromatin interaction
ENSG00000273013	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs2101285	0.92[ASN][1000 genomes]
rs2341399	0.92[ASN][1000 genomes]
rs6763760	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003194	chr3:195960270-196342423	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv536894	chr3:195960270-196342423	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	nsv1003066	chr3:196098763-196414159	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
4	esv2752687	chr3:196147690-196286690	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv948681	chr3:196148055-197007546	Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
6	nsv1010483	chr3:196210054-196319543	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
7	nsv536896	chr3:196210054-196319543	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
8	nsv1014692	chr3:196242249-196531824	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
9	esv2763750	chr3:196242261-196278366	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:196239400-196245000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr3:196241400-196244600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr3:196242600-196245200	Enhancers	Skeletal Muscle Male	skeletal muscle
4	chr3:196242600-196246400	Enhancers	K562	blood
5	chr3:196244000-196245400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr3:196244000-196245400	Enhancers	HMEC	breast
7	chr3:196244200-196244800	Active TSS	iPS-20b Cell Line	embryonic stem cell
8	chr3:196244200-196246800	Enhancers	Hela-S3	cervix
9	chr3:196244400-196244600	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr3:196244400-196245600	Weak transcription	Skeletal Muscle Female	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links