Variant report

Variant	rs4272759
Chromosome Location	chr11:101394541-101394542
allele	G/T
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	FOS	chr11:101394450-101394728	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr11:101394440-101394676	MCF10A-Er-Src	breast:	n/a	n/a
3	FOS	chr11:101394455-101394649	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:101367288..101368830-chr11:101394227..101396283,2	K562	blood:
2	chr11:101383577..101385608-chr11:101393235..101396099,2	MCF-7	breast:

Variant related genes	Relation type
MIR3920	TF binding region

Extended variants
information (count: 68 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10501979	0.84[ASN][1000 genomes]
rs10501980	1.00[CHB][hapmap];0.88[CHD][hapmap]
rs10501981	1.00[CHB][hapmap]
rs10501986	1.00[CHB][hapmap];0.88[CHD][hapmap]
rs10750606	0.91[CHB][hapmap]
rs10791477	0.90[CHB][hapmap]
rs10791478	0.90[CHB][hapmap];0.88[CHD][hapmap]
rs10791479	1.00[CHB][hapmap]
rs10791481	1.00[CHB][hapmap]
rs10791485	1.00[CHB][hapmap];0.92[CHD][hapmap]
rs10791486	0.91[CHB][hapmap]
rs10791487	1.00[CHB][hapmap]
rs10791490	1.00[CHB][hapmap];0.88[CHD][hapmap]
rs10895118	0.90[CHB][hapmap]
rs10895119	0.82[CHB][hapmap]
rs10895121	0.90[CHB][hapmap]
rs10895122	0.90[CHB][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs10895123	0.91[CHB][hapmap]
rs10895124	1.00[CHB][hapmap];0.90[CHD][hapmap]
rs10895125	1.00[CHB][hapmap];0.92[CHD][hapmap]
rs10895126	0.91[CHB][hapmap]
rs10895127	0.91[CHB][hapmap];0.92[CHD][hapmap]
rs10895128	0.90[CHB][hapmap]
rs11224790	1.00[CHB][hapmap]
rs11224791	1.00[CHB][hapmap];0.88[CHD][hapmap]
rs11224792	1.00[CHB][hapmap];0.91[CHD][hapmap]
rs11224800	1.00[CHB][hapmap]
rs11224801	1.00[CHB][hapmap]
rs11224802	1.00[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs11224806	1.00[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];0.92[ASN][1000 genomes]
rs11224807	0.89[ASN][1000 genomes]
rs11224808	0.92[ASN][1000 genomes]
rs17674687	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs17741661	0.91[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs17742220	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4129253	0.90[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs4129254	0.90[CHB][hapmap]
rs4129255	0.90[CHB][hapmap];0.91[CHD][hapmap]
rs4262694	1.00[CHB][hapmap]
rs4275596	0.91[CHB][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes]
rs4285844	0.91[CHB][hapmap];0.92[CHD][hapmap]
rs4331056	0.91[CHB][hapmap]
rs4403777	0.90[CHB][hapmap];0.88[CHD][hapmap]
rs4477408	1.00[CHB][hapmap]
rs4481994	0.91[CHB][hapmap];0.92[CHD][hapmap]
rs4492783	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4542378	1.00[CHB][hapmap]
rs6590870	1.00[CHB][hapmap];0.87[CHD][hapmap]
rs6590872	0.82[CHB][hapmap]
rs6590874	1.00[CHB][hapmap]
rs6590877	1.00[CHB][hapmap]
rs7115999	0.91[CHB][hapmap];0.87[CHD][hapmap]
rs7116473	0.90[CHB][hapmap]
rs7123199	0.91[CHB][hapmap]
rs7127243	0.91[CHB][hapmap];0.92[CHD][hapmap]
rs7925012	0.91[CHB][hapmap];0.92[CHD][hapmap]
rs7927661	1.00[CHB][hapmap]
rs7927852	0.91[CHB][hapmap]
rs7927859	0.91[CHB][hapmap];0.92[CHD][hapmap]
rs7932871	1.00[CHB][hapmap];0.91[CHD][hapmap]
rs7934116	0.90[CHB][hapmap]
rs7934208	1.00[CHB][hapmap];0.92[CHD][hapmap]
rs7934219	1.00[CHB][hapmap]
rs7935702	1.00[CHB][hapmap]
rs7937745	0.91[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv556131	chr11:100985777-101480017	Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
2	nsv530644	chr11:101010088-101486038	Strong transcription Weak transcription Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
3	nsv898330	chr11:101243644-101722031	Enhancers Bivalent/Poised TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4272759	MMP20	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:101387600-101400800	Weak transcription	Ovary	ovary
2	chr11:101392400-101402600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr11:101392600-101394600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr11:101393600-101395400	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr11:101393600-101395800	Weak transcription	Fetal Intestine Large	intestine
6	chr11:101393600-101396600	Weak transcription	Fetal Intestine Small	intestine
7	chr11:101394000-101395000	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr11:101394200-101394600	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr11:101394200-101395000	Enhancers	iPS-20b Cell Line	embryonic stem cell
10	chr11:101394200-101395800	Weak transcription	Primary B cells from peripheral blood	blood
11	chr11:101394400-101394600	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr11:101394400-101394800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr11:101394400-101395000	Enhancers	iPS-18 Cell Line	embryonic stem cell

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