Variant report

Variant	rs28580295
Chromosome Location	chr4:120278873-120278874
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 150 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:139)

rs_ID	r²[population]
rs10003567	0.86[CHB][hapmap]
rs10006259	0.86[CHB][hapmap]
rs10006525	0.86[CHB][hapmap];0.93[CHD][hapmap];0.81[JPT][hapmap]
rs10006706	0.86[CHB][hapmap];0.93[CHD][hapmap];0.81[JPT][hapmap]
rs10006877	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs10009626	0.80[JPT][hapmap]
rs10012456	0.84[ASN][1000 genomes]
rs10013042	0.81[CHB][hapmap]
rs10013305	0.86[CHB][hapmap];0.89[CHD][hapmap];0.81[JPT][hapmap]
rs10017335	0.86[CHB][hapmap];0.93[CHD][hapmap];0.81[JPT][hapmap]
rs10017371	0.84[ASN][1000 genomes]
rs10018280	0.85[CHB][hapmap]
rs10019674	0.81[CHB][hapmap];0.89[CHD][hapmap];0.81[JPT][hapmap]
rs10020034	0.81[ASN][1000 genomes]
rs1002152	0.84[ASN][1000 genomes]
rs10024844	0.80[ASN][1000 genomes]
rs10025054	0.80[ASN][1000 genomes]
rs10026436	0.84[ASN][1000 genomes]
rs10028669	0.83[ASN][1000 genomes]
rs10030660	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs10031483	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs10031718	0.81[ASN][1000 genomes]
rs1010739	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs1010740	0.86[CHB][hapmap];0.86[CHD][hapmap];0.81[JPT][hapmap]
rs1011054	0.95[CHD][hapmap]
rs10518300	0.86[CHB][hapmap];0.95[CHD][hapmap]
rs10518328	0.86[CHB][hapmap];0.93[CHD][hapmap];0.81[JPT][hapmap]
rs1052633	0.92[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];0.81[MEX][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes]
rs11098498	0.92[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap]
rs11098499	0.81[CHB][hapmap];0.95[CHD][hapmap]
rs11098501	0.86[CHB][hapmap]
rs11098531	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs1155576	0.81[CHB][hapmap];0.89[CHD][hapmap];0.81[JPT][hapmap]
rs11722183	0.82[ASN][1000 genomes]
rs11723550	0.82[EUR][1000 genomes]
rs11724758	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11728730	0.84[ASN][1000 genomes]
rs11729521	0.86[CHB][hapmap];0.93[CHD][hapmap];0.80[JPT][hapmap]
rs11729991	0.84[ASN][1000 genomes]
rs11731571	0.94[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs11731756	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs11732621	0.92[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];0.81[MEX][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs11732686	0.88[CHB][hapmap]
rs11734241	0.86[CHB][hapmap];0.93[CHD][hapmap];0.81[JPT][hapmap]
rs11737400	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11933966	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs11935596	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs11944880	0.95[CHD][hapmap]
rs11947234	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs12498599	0.86[CHB][hapmap];0.86[CHD][hapmap];0.81[JPT][hapmap]
rs12502423	0.86[CHB][hapmap];0.89[CHD][hapmap];0.81[JPT][hapmap]
rs12507565	0.86[CHB][hapmap]
rs12507964	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs12508504	0.86[CHB][hapmap];0.93[CHD][hapmap];0.81[JPT][hapmap]
rs12510138	0.86[CHB][hapmap];0.91[CHD][hapmap];0.81[JPT][hapmap]
rs12511640	0.86[CHB][hapmap]
rs12512118	0.81[ASN][1000 genomes]
rs12513083	0.86[CHB][hapmap]
rs12711071	0.86[CHB][hapmap];0.95[CHD][hapmap]
rs13104219	0.86[CHB][hapmap];0.80[JPT][hapmap]
rs13104396	0.84[ASN][1000 genomes]
rs13108589	0.81[ASN][1000 genomes]
rs13113112	0.95[CHD][hapmap]
rs13113885	0.81[EUR][1000 genomes]
rs13128602	0.86[CHB][hapmap];0.86[CHD][hapmap];0.81[JPT][hapmap]
rs13134517	0.82[CHB][hapmap]
rs13134665	0.81[CHB][hapmap];0.89[CHD][hapmap];0.81[JPT][hapmap]
rs13149954	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13150541	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1383532	0.86[CHB][hapmap];0.91[CHD][hapmap];0.81[JPT][hapmap]
rs1480931	0.86[CHB][hapmap];0.93[CHD][hapmap];0.81[JPT][hapmap]
rs1480936	0.81[CHB][hapmap];0.84[CHD][hapmap];0.80[JPT][hapmap]
rs1480940	0.86[CHB][hapmap];0.86[CHD][hapmap];0.80[JPT][hapmap]
rs1511017	0.86[CHB][hapmap]
rs1511018	0.95[CHD][hapmap]
rs1511019	0.95[CHD][hapmap]
rs1511025	0.86[CHB][hapmap];0.95[CHD][hapmap];0.81[JPT][hapmap]
rs1546502	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs1546503	0.86[CHB][hapmap]
rs1546505	0.86[CHB][hapmap];0.98[CHD][hapmap];0.86[JPT][hapmap]
rs1552095	0.86[CHB][hapmap];0.89[CHD][hapmap];0.81[JPT][hapmap]
rs17006190	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs1980025	0.86[CHB][hapmap];0.95[CHD][hapmap]
rs1980026	0.86[CHB][hapmap]
rs2036858	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2175383	0.81[EUR][1000 genomes]
rs2291185	0.81[CHB][hapmap];0.91[CHD][hapmap];0.81[JPT][hapmap]
rs2306456	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs2389803	0.86[CHB][hapmap];0.93[CHD][hapmap];0.81[JPT][hapmap]
rs2389809	0.86[CHB][hapmap];0.80[JPT][hapmap]
rs28403131	0.84[ASN][1000 genomes]
rs28633994	0.83[ASN][1000 genomes]
rs2892848	0.86[CHB][hapmap];0.93[CHD][hapmap];0.81[JPT][hapmap]
rs3733519	0.89[CHB][hapmap];0.83[JPT][hapmap]
rs3733524	0.81[CHB][hapmap];0.91[CHD][hapmap];0.81[JPT][hapmap]
rs3749591	0.93[CHD][hapmap]
rs3775841	0.80[JPT][hapmap]
rs3775843	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs3775844	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs3775845	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs3775848	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs3775852	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs3822192	0.81[CHB][hapmap];0.89[CHD][hapmap];0.81[JPT][hapmap]
rs3822194	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs3822195	0.82[CHB][hapmap]
rs3864141	0.81[ASN][1000 genomes]
rs59394118	0.83[ASN][1000 genomes]
rs62320739	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62320740	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6534139	0.86[CHB][hapmap];0.91[CHD][hapmap];0.81[JPT][hapmap]
rs6822808	0.90[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap]
rs6834796	0.86[CHB][hapmap];0.91[CHD][hapmap];0.81[JPT][hapmap]
rs6835635	0.86[CHB][hapmap];0.88[CHD][hapmap];0.81[JPT][hapmap]
rs6837898	0.95[CHD][hapmap]
rs6838617	0.81[ASN][1000 genomes]
rs6843229	0.86[CHB][hapmap]
rs6843509	0.92[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];0.81[MEX][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs6847075	0.83[ASN][1000 genomes]
rs6848389	0.86[CHB][hapmap];0.93[CHD][hapmap];0.80[JPT][hapmap]
rs6848580	0.83[ASN][1000 genomes]
rs6849171	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs6849561	0.86[CHB][hapmap];0.91[CHD][hapmap];0.81[JPT][hapmap]
rs6849889	0.81[CHB][hapmap];0.95[CHD][hapmap]
rs6853998	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs714899	0.86[CHB][hapmap]
rs7659501	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs7672594	0.86[CHB][hapmap];0.95[CHD][hapmap]
rs7681544	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs7687843	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs7688802	0.85[CHB][hapmap];0.80[JPT][hapmap]
rs7695620	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs7699064	0.86[CHB][hapmap];0.89[CHD][hapmap];0.81[JPT][hapmap]
rs878372	0.86[CHB][hapmap];0.95[CHD][hapmap]
rs907205	0.86[CHB][hapmap]
rs9991959	0.86[CHB][hapmap];0.95[CHD][hapmap]
rs9997631	0.84[CHB][hapmap];0.81[JPT][hapmap]
rs9998585	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs9998953	0.81[ASN][1000 genomes]
rs9999724	0.81[CHB][hapmap];0.95[CHD][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	nsv916641	chr4:119780023-120777320	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv1012868	chr4:120014630-120464880	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv537232	chr4:120014630-120464880	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
4	nsv428769	chr4:120205572-120363323	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv879841	chr4:120244085-120388406	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv879842	chr4:120244085-120424087	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv427694	chr4:120250511-120501728	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	esv2538163	chr4:120252854-120388678	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	nsv964091	chr4:120255342-120290951	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region	2 gene(s)	inside rSNPs	diseases
10	esv3512786	chr4:120275104-120279402	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases
11	esv3512787	chr4:120275104-120279402	Enhancers Weak transcription	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs28580295	USP53	cis	parietal	SCAN
rs28580295	BBS7	cis	parietal	SCAN
rs28580295	TRPC3	cis	parietal	SCAN
rs28580295	LOC645513	Cis_1M	lymphoblastoid	RTeQTL
rs28580295	FLJ14186///LOC284701///LOC441124///LOC728624	Cis_1M	lymphoblastoid	RTeQTL
rs28580295	RP11-33B1.1	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120269600-120293000	Weak transcription	Fetal Heart	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links