Variant report

Variant	rs399104
Chromosome Location	chr5:80975470-80975471
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	chr5:80971757..80974379-chr5:80975193..80977880,3	K562	blood:
2	chr5:80970290..80973257-chr5:80975148..80979422,4	K562	blood:

Extended variants
information (count: 46 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1023747	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.84[GIH][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1095605	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11957810	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.95[MEX][hapmap];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1347597	0.92[CEU][hapmap]
rs1436498	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1436499	1.00[CHB][hapmap]
rs2043646	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2917542	1.00[CHB][hapmap];0.85[CHD][hapmap]
rs365147	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs380946	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs382297	1.00[CHB][hapmap];0.85[CHD][hapmap]
rs384433	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs385332	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs385716	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs390171	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs402352	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs406292	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs411520	0.80[EUR][1000 genomes]
rs413472	1.00[CHB][hapmap]
rs418033	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs419017	0.96[CEU][hapmap];1.00[CHB][hapmap];0.84[GIH][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs421348	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs432617	0.81[EUR][1000 genomes]
rs435901	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs437417	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs438128	0.86[EUR][1000 genomes]
rs445253	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs446064	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs446565	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs447574	0.81[CEU][hapmap];0.93[ASN][1000 genomes]
rs452314	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs453068	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs454487	0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs585558	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs682481	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6898782	0.85[CHB][hapmap]
rs724913	1.00[CHB][hapmap];0.85[CHD][hapmap]
rs827065	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs863772	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]

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	nsv882233	chr5:80849084-81049187	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv882235	chr5:80909132-81006061	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv830361	chr5:80909811-81080409	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv882236	chr5:80930992-80999768	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv882237	chr5:80938489-81006061	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
6	esv3345018	chr5:80972245-80998709	ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
7	esv3330268	chr5:80972245-81001669	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:80921200-80983000	Weak transcription	Aorta	Aorta
2	chr5:80945600-80985400	Weak transcription	Fetal Kidney	kidney
3	chr5:80950200-80975600	Weak transcription	Thymus	Thymus
4	chr5:80963400-80983200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr5:80963400-80983400	Weak transcription	Left Ventricle	heart
6	chr5:80963400-80983800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr5:80967400-80980000	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr5:80967400-80991400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr5:80971200-80995800	Weak transcription	HSMMtube	muscle
10	chr5:80972600-80977000	Weak transcription	Fetal Thymus	thymus
11	chr5:80973400-80990000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr5:80973600-80976000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
13	chr5:80973800-80978800	Weak transcription	Dnd41	blood
14	chr5:80973800-80980400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr5:80974000-80975600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr5:80974800-80984200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr5:80975400-80976000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links