Variant report

Variant	rs1492272
Chromosome Location	chr3:119962322-119962323
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:119961553..119963645-chr3:120067756..120069896,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LRRC58-4	chr3:119961707-119962623	NONHSAT091433

Variant related genes	Relation type
ENSG00000240661	Chromatin interaction
ENSG00000163428	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1056928	1.00[JPT][hapmap]
rs1147696	1.00[JPT][hapmap]
rs1147698	1.00[JPT][hapmap]
rs1147699	1.00[JPT][hapmap]
rs12494395	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1259328	1.00[JPT][hapmap]
rs13061630	1.00[JPT][hapmap]
rs13073885	1.00[JPT][hapmap]
rs13081675	1.00[JPT][hapmap]
rs13081694	1.00[JPT][hapmap]
rs13091848	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13096256	1.00[JPT][hapmap]
rs13097755	1.00[JPT][hapmap]
rs13100865	1.00[JPT][hapmap]
rs13709	1.00[JPT][hapmap]
rs1515577	1.00[JPT][hapmap]
rs17813772	1.00[JPT][hapmap]
rs1969356	1.00[JPT][hapmap]
rs2029607	1.00[JPT][hapmap]
rs2030414	1.00[JPT][hapmap]
rs2091726	1.00[JPT][hapmap]
rs2272515	1.00[JPT][hapmap]
rs2319670	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2488	1.00[JPT][hapmap]
rs34014378	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34829073	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34964758	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34998142	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35193138	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35964791	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4146299	0.96[CEU][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4146300	0.96[CEU][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4676676	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4676698	1.00[JPT][hapmap]
rs4676703	1.00[JPT][hapmap]
rs4676776	1.00[JPT][hapmap]
rs4676778	1.00[JPT][hapmap]
rs4676779	1.00[JPT][hapmap]
rs4676781	1.00[JPT][hapmap]
rs4676782	1.00[JPT][hapmap]
rs4676783	1.00[JPT][hapmap]
rs4676811	1.00[JPT][hapmap]
rs55861253	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56103727	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6438574	0.83[ASN][1000 genomes]
rs6438575	1.00[JPT][hapmap]
rs6771116	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6776878	1.00[JPT][hapmap]
rs6792814	1.00[JPT][hapmap]
rs7612000	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs869247	1.00[JPT][hapmap]
rs9843220	0.82[CEU][hapmap]
rs9880550	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949589	chr3:119560606-120175917	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1001476	chr3:119575386-120075417	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
3	nsv536704	chr3:119575386-120075417	Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
4	nsv877376	chr3:119824037-120119446	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv1007557	chr3:119892894-120764353	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	nsv536706	chr3:119892894-120764353	Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
7	nsv829698	chr3:119960869-120129126	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119959400-119962800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr3:119960000-119963200	Weak transcription	Fetal Stomach	stomach
3	chr3:119960000-119963600	Weak transcription	Fetal Brain Female	brain
4	chr3:119960000-119963800	Weak transcription	Fetal Brain Male	brain
5	chr3:119960800-119963600	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr3:119961200-119962800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
7	chr3:119961200-119962800	Weak transcription	Fetal Muscle Leg	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links