Variant report

Variant	rs4676776
Chromosome Location	chr3:120106539-120106540
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:120066467..120068992-chr3:120105411..120108399,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000240661	Chromatin interaction
ENSG00000163428	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1056928	1.00[JPT][hapmap]
rs1147696	1.00[JPT][hapmap]
rs1147698	1.00[JPT][hapmap]
rs1147699	1.00[JPT][hapmap]
rs12173	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12192	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1259328	1.00[JPT][hapmap]
rs13061630	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13070508	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13081675	0.88[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13081694	0.88[CEU][hapmap];1.00[JPT][hapmap]
rs13083670	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13096232	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13096256	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13096973	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13097755	0.88[CEU][hapmap];1.00[JPT][hapmap]
rs13100865	0.82[ASW][hapmap];0.88[CEU][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13709	1.00[JPT][hapmap]
rs1492272	1.00[JPT][hapmap]
rs1515577	1.00[JPT][hapmap]
rs17813772	0.92[CEU][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1969356	1.00[JPT][hapmap]
rs2029607	1.00[JPT][hapmap]
rs2030414	1.00[JPT][hapmap]
rs2091726	0.92[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2201166	1.00[ASN][1000 genomes]
rs2272515	0.88[CEU][hapmap];1.00[JPT][hapmap]
rs2488	1.00[JPT][hapmap]
rs33935225	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34134493	1.00[ASN][1000 genomes]
rs34805176	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35587339	1.00[ASN][1000 genomes]
rs36001904	0.84[AMR][1000 genomes]
rs36068602	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3755558	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4146299	1.00[JPT][hapmap]
rs4146300	1.00[JPT][hapmap]
rs4676696	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4676698	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4676765	1.00[ASN][1000 genomes]
rs4676768	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4676777	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4676778	1.00[JPT][hapmap]
rs4676779	1.00[JPT][hapmap]
rs4676781	0.82[ASW][hapmap];0.92[CEU][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4676782	0.92[CEU][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4676783	0.92[CEU][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap]
rs6438575	0.82[ASW][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs66815350	1.00[ASN][1000 genomes]
rs6767463	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6770270	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6803846	1.00[ASN][1000 genomes]
rs71327229	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs869247	1.00[JPT][hapmap]
rs9880550	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 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	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
3	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
4	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
5	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
6	nsv1012127	chr3:120015620-120272893	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Active 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	26 gene(s)	inside rSNPs	diseases
7	nsv536707	chr3:120015620-120272893	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh 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	26 gene(s)	inside rSNPs	diseases
8	nsv1006428	chr3:120015620-120421982	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
9	esv3369381	chr3:120066425-120425510	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
10	esv3350409	chr3:120066445-120425480	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
11	nsv3968	chr3:120066454-120111463	Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4676776	GTF2E1	cis	cerebellum	SCAN
rs4676776	RABL3	cis	cerebellum	SCAN
rs4676776	CD80	cis	cerebellum	SCAN
rs4676776	C3orf1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:120090600-120112600	Weak transcription	Aorta	Aorta
2	chr3:120096800-120112600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:120103400-120112400	Weak transcription	Colon Smooth Muscle	Colon
4	chr3:120103600-120113400	Weak transcription	Right Ventricle	heart
5	chr3:120104200-120112200	Weak transcription	Left Ventricle	heart
6	chr3:120105400-120112400	Weak transcription	NHLF	lung
7	chr3:120106000-120112200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links