Variant report

Variant	rs56839556
Chromosome Location	chr3:161141373-161141374
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	SMC3	chr3:161141320-161142233	SK-N-SH	brain:	n/a	chr3:161141894-161141908
2	RAD21	chr3:161141369-161142307	Hela-S3	cervix:	n/a	chr3:161141890-161141909 chr3:161141896-161141905
3	CTCF	chr3:161141194-161142313	A549	lung:	n/a	chr3:161141887-161141908 chr3:161141892-161141910 chr3:161141893-161141909 chr3:161141898-161141907 chr3:161141895-161141905

No.	Distal block	Cell Line	Cell type
1	chr3:161137822..161140079-chr3:161140327..161142102,2	MCF-7	breast:
2	chr3:160819430..160825093-chr3:161138517..161141726,6	MCF-7	breast:
3	chr3:160784766..160787646-chr3:161137298..161141604,4	MCF-7	breast:
4	chr3:160991166..160991884-chr3:161141198..161141933,2	MCF-7	breast:
5	chr3:160472661..160475236-chr3:161140062..161142402,3	MCF-7	breast:
6	chr3:161137896..161142184-chr3:161162436..161166379,4	MCF-7	breast:
7	chr3:160927027..160929410-chr3:161139082..161141538,2	MCF-7	breast:
8	chr3:160934874..160951087-chr3:161118055..161142485,77	MCF-7	breast:
9	chr3:161139841..161141784-chr3:161148719..161150343,2	MCF-7	breast:
10	chr3:161007555..161015806-chr3:161127103..161142651,19	MCF-7	breast:
11	chr3:160938218..160944428-chr3:161134456..161142008,22	MCF-7	breast:
12	chr3:160990988..160993018-chr3:161141247..161142690,7	MCF-7	breast:
13	chr3:161139368..161142098-chr3:161277561..161279557,2	MCF-7	breast:
14	chr3:160814710..160815272-chr3:161141334..161141969,2	K562	blood:

Variant related genes	Relation type
ENSG00000240567	TF binding region
ENSG00000271052	Chromatin interaction
ENSG00000260572	Chromatin interaction
ENSG00000169255	Chromatin interaction
ENSG00000169251	Chromatin interaction
ENSG00000163590	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs12486111	0.94[ASN][1000 genomes]
rs12486998	0.94[ASN][1000 genomes]
rs12487002	0.94[ASN][1000 genomes]
rs12488127	0.94[ASN][1000 genomes]
rs12491623	0.90[ASN][1000 genomes]
rs12494520	0.90[ASN][1000 genomes]
rs1450518	0.94[ASN][1000 genomes]
rs2035499	0.88[ASN][1000 genomes]
rs58851337	0.90[ASN][1000 genomes]
rs58892449	0.88[ASN][1000 genomes]
rs59193340	0.84[ASN][1000 genomes]
rs59368066	0.90[ASN][1000 genomes]
rs62279930	0.81[EUR][1000 genomes]
rs62279931	0.81[EUR][1000 genomes]
rs62279948	0.86[EUR][1000 genomes]
rs62279949	0.86[EUR][1000 genomes]
rs62279950	0.86[EUR][1000 genomes]
rs62279954	0.94[EUR][1000 genomes]
rs62279955	0.94[EUR][1000 genomes]
rs6787697	0.84[ASN][1000 genomes]
rs73162598	0.94[EUR][1000 genomes]
rs73878323	0.94[ASN][1000 genomes]
rs73878329	0.94[ASN][1000 genomes]
rs7614130	0.94[ASN][1000 genomes]
rs7629841	0.81[ASN][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	nsv931072	chr3:160669567-161159779	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh 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	98 gene(s)	inside rSNPs	diseases
2	nsv533237	chr3:161019834-161804660	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	91 gene(s)	inside rSNPs	diseases
3	nsv829772	chr3:161047817-161202554	Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	88 gene(s)	inside rSNPs	diseases
4	nsv877710	chr3:161087857-161245414	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	84 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:161134400-161145200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:161134400-161148200	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr3:161137200-161141400	Enhancers	HepG2	liver
4	chr3:161138000-161141400	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr3:161139200-161141400	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr3:161139200-161141400	Enhancers	iPS-20b Cell Line	embryonic stem cell
7	chr3:161139200-161141600	Enhancers	iPS-18 Cell Line	embryonic stem cell
8	chr3:161139200-161141800	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr3:161139200-161143600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:161139400-161141400	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr3:161139400-161141600	Enhancers	HUES48 Cell Line	embryonic stem cell
12	chr3:161140200-161141400	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr3:161140200-161145400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr3:161140400-161143800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr3:161141000-161141400	Enhancers	H1 Cell Line	embryonic stem cell
16	chr3:161141200-161141400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr3:161141200-161141400	Enhancers	Brain Hippocampus Middle	brain
18	chr3:161141200-161141600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr3:161141200-161144800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links