Variant report

Variant	rs629079
Chromosome Location	chr1:72346331-72346332
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11209854	0.80[CHB][hapmap]
rs11209861	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11209862	0.86[CEU][hapmap]
rs11209864	0.90[CEU][hapmap];0.83[EUR][1000 genomes]
rs11209867	0.86[CEU][hapmap]
rs12025922	0.86[CEU][hapmap];0.84[EUR][1000 genomes]
rs12045130	0.86[CEU][hapmap];0.81[MEX][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12562379	0.86[CEU][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12749167	0.86[CEU][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12749550	0.85[CEU][hapmap]
rs1350648	0.80[CHB][hapmap]
rs1426179	0.86[CEU][hapmap];0.81[MEX][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1648263	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17091869	0.81[EUR][1000 genomes]
rs17091876	0.85[CEU][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1765607	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs35285032	0.84[EUR][1000 genomes]
rs3851882	0.85[CEU][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3909664	0.86[CEU][hapmap];0.83[EUR][1000 genomes]
rs474680	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs495411	0.80[CHB][hapmap]
rs499314	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs508954	0.80[CHB][hapmap]
rs514435	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs516876	0.95[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs517901	0.80[CHB][hapmap]
rs518523	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs545538	0.80[CHB][hapmap]
rs554161	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs577867	0.96[ASN][1000 genomes]
rs591540	0.81[CHD][hapmap]
rs618293	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs626185	0.86[CEU][hapmap];0.80[EUR][1000 genomes]
rs628247	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs648556	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs652213	1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[YRI][hapmap];0.93[ASN][1000 genomes]
rs6683443	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6683448	0.80[CHB][hapmap]
rs67094512	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007250	chr1:71998391-72350683	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv534992	chr1:71998391-72350683	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv948821	chr1:72049987-72477221	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1003446	chr1:72060680-72419918	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv817447	chr1:72098815-72558020	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv1008210	chr1:72099161-72374197	ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv916783	chr1:72196061-72707953	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv1007910	chr1:72247302-72543998	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	esv2762150	chr1:72271227-72395953	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv870762	chr1:72300968-72376262	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases
11	nsv871908	chr1:72315820-72370014	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases
12	nsv999162	chr1:72319163-72477496	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
13	nsv534995	chr1:72319163-72477496	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:72344000-72347000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr1:72344200-72347200	Weak transcription	HSMMtube	muscle
3	chr1:72344200-72347600	Weak transcription	HSMM	muscle
4	chr1:72344600-72347400	Weak transcription	Fetal Heart	heart
5	chr1:72344800-72351000	Enhancers	Dnd41	blood
6	chr1:72345000-72347600	Enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr1:72345000-72347600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr1:72345400-72348400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr1:72345400-72349000	Enhancers	Pancreatic Islets	Pancreatic Islet
10	chr1:72345800-72347000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr1:72346000-72347800	Enhancers	Primary hematopoietic stem cells	blood
12	chr1:72346000-72349200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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