Variant report

Variant	rs1480
Chromosome Location	chr6:55960989-55960990
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	EP300	chr6:55960971-55961744	SK-N-SH_RA	brain:	n/a	n/a
2	EP300	chr6:55960942-55961647	SK-N-SH_RA	brain:	n/a	n/a
3	POLR2A	chr6:55960978-55962139	SK-N-MC	brain:	n/a	n/a

Variant related genes	Relation type
COL21A1	TF binding region

Extended variants
information (count: 93 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs1022539	0.92[CHB][hapmap];0.82[CHD][hapmap]
rs1033478	0.83[CEU][hapmap];0.84[CHB][hapmap]
rs1205109	0.82[EUR][1000 genomes]
rs12199712	0.92[CHB][hapmap]
rs12199742	0.92[CHB][hapmap];0.82[CHD][hapmap]
rs1319111	0.84[CHB][hapmap]
rs1319112	0.82[CEU][hapmap];0.83[MEX][hapmap];0.80[TSI][hapmap]
rs13193925	0.83[CEU][hapmap];1.00[CHB][hapmap]
rs13209836	0.92[CHB][hapmap]
rs1555097	1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[EUR][1000 genomes]
rs1925141	0.83[CEU][hapmap];0.83[MEX][hapmap];0.80[TSI][hapmap]
rs1925143	0.92[CHB][hapmap]
rs1925147	0.83[CEU][hapmap]
rs1925149	0.82[CHB][hapmap]
rs1925177	0.82[EUR][1000 genomes]
rs1925179	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs1925181	0.88[CHB][hapmap]
rs1925185	0.80[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.83[MEX][hapmap]
rs1925189	0.92[CHB][hapmap]
rs1980487	0.92[CHB][hapmap];0.82[CHD][hapmap]
rs2038149	0.92[CHB][hapmap];0.82[CHD][hapmap]
rs2038173	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2206674	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2328677	0.95[CEU][hapmap];0.81[CHB][hapmap];0.94[CHD][hapmap];0.94[TSI][hapmap]
rs2397204	0.95[CEU][hapmap];1.00[CHB][hapmap]
rs2397208	0.92[CHB][hapmap]
rs2745366	1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[EUR][1000 genomes]
rs2764046	1.00[CEU][hapmap];0.90[CHB][hapmap]
rs2764048	0.83[EUR][1000 genomes]
rs2764052	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2764055	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2764056	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2764059	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2840989	0.83[EUR][1000 genomes]
rs2840990	0.83[EUR][1000 genomes]
rs2841000	0.83[CEU][hapmap];0.92[CHB][hapmap];0.93[CHD][hapmap];0.83[MEX][hapmap];0.80[TSI][hapmap]
rs2841006	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2841007	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3817983	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3846918	1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[EUR][1000 genomes]
rs3846920	1.00[CEU][hapmap];0.84[CHB][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3846921	0.95[CEU][hapmap];0.82[CHB][hapmap]
rs3846922	0.92[CHB][hapmap];0.82[CHD][hapmap]
rs3846923	0.81[CHB][hapmap]
rs3846924	0.83[CHB][hapmap]
rs3857611	0.83[CEU][hapmap];0.83[MEX][hapmap];0.80[TSI][hapmap]
rs3857612	0.82[CHB][hapmap]
rs3996940	0.91[CEU][hapmap];0.82[CHB][hapmap];0.81[GIH][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap]
rs4119567	0.92[CHB][hapmap];0.82[CHD][hapmap]
rs4126558	0.91[CHB][hapmap]
rs4379279	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4495274	0.92[CHB][hapmap];0.82[CHD][hapmap]
rs4573075	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4596475	1.00[CEU][hapmap];0.82[CHB][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4599643	0.93[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4712113	0.80[CEU][hapmap];0.91[CHB][hapmap]
rs4715574	0.83[EUR][1000 genomes]
rs4715575	0.83[EUR][1000 genomes]
rs4715585	0.92[CHB][hapmap]
rs4715591	0.83[CEU][hapmap];0.92[CHB][hapmap];0.82[CHD][hapmap]
rs4715597	0.83[CEU][hapmap]
rs6459124	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6459128	0.92[CHB][hapmap]
rs6459133	0.92[CHB][hapmap];0.87[CHD][hapmap]
rs6459136	0.92[CHB][hapmap]
rs66585712	0.97[EUR][1000 genomes]
rs66953461	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6909268	0.90[CEU][hapmap]
rs6914495	0.92[CHB][hapmap];0.82[CHD][hapmap]
rs6927919	1.00[CEU][hapmap];0.82[CHB][hapmap];0.80[EUR][1000 genomes]
rs6933151	0.92[CHB][hapmap]
rs6939465	0.92[CHB][hapmap]
rs6941673	0.83[EUR][1000 genomes]
rs7774374	0.87[CEU][hapmap];0.84[CHB][hapmap]
rs9296824	0.83[EUR][1000 genomes]
rs9296828	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9296830	0.84[CEU][hapmap];1.00[CHB][hapmap]
rs9357886	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9357891	0.95[CEU][hapmap];1.00[CHB][hapmap]
rs9367673	0.83[EUR][1000 genomes]
rs9370485	1.00[CHB][hapmap]
rs9370486	0.92[CHB][hapmap]
rs9382583	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs9382595	0.82[CHB][hapmap]
rs9396176	1.00[CHB][hapmap]
rs9475560	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9475593	0.91[CHB][hapmap]
rs9475621	0.92[CHB][hapmap];0.82[CHD][hapmap]
rs994667	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap]

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	nsv1034037	chr6:55222409-56069600	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv885911	chr6:55789704-56143231	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv526703	chr6:55810482-56023811	Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
4	nsv1029182	chr6:55910866-55991956	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:55920600-56018400	Weak transcription	Ovary	ovary
2	chr6:55933200-55961000	Weak transcription	Placenta	Placenta
3	chr6:55956600-55961200	Weak transcription	HUVEC	blood vessel
4	chr6:55956600-55961400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr6:55956600-55965800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr6:55956600-55978400	Weak transcription	Aorta	Aorta
7	chr6:55956800-55965600	Weak transcription	NHLF	lung
8	chr6:55957800-55962200	Enhancers	Primary neutrophils fromperipheralblood	blood
9	chr6:55958200-55961200	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr6:55958200-55965600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr6:55958600-55962200	Strong transcription	Fetal Muscle Trunk	muscle
12	chr6:55959400-55961400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr6:55959600-55961200	Enhancers	Monocytes-CD14+_RO01746	blood
14	chr6:55959600-55969600	Weak transcription	Fetal Lung	lung
15	chr6:55960600-55977800	Weak transcription	Fetal Muscle Leg	muscle
16	chr6:55960600-55978000	Weak transcription	Stomach Smooth Muscle	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links