Variant report

Variant	rs1860684
Chromosome Location	chr7:146060608-146060609
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1005386	1.00[CHB][hapmap]
rs1005387	1.00[CHB][hapmap];0.87[CHD][hapmap]
rs1005388	1.00[CHB][hapmap];0.84[CHD][hapmap]
rs10226754	0.86[CEU][hapmap];1.00[CHB][hapmap]
rs10238194	0.91[MEX][hapmap]
rs10262298	0.81[AMR][1000 genomes]
rs12703801	0.91[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap];0.95[TSI][hapmap]
rs12703802	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12703803	1.00[CHB][hapmap]
rs13223832	1.00[CHB][hapmap]
rs13235449	0.86[CHB][hapmap]
rs1639477	0.81[AMR][1000 genomes]
rs1639480	0.81[CEU][hapmap]
rs1639481	0.95[MEX][hapmap];0.82[AMR][1000 genomes]
rs1639482	0.81[AMR][1000 genomes]
rs1639483	0.82[AMR][1000 genomes]
rs17170057	1.00[CHB][hapmap]
rs17170068	0.86[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap]
rs17170069	1.00[CHB][hapmap]
rs1718076	0.81[AMR][1000 genomes]
rs1724528	0.87[MEX][hapmap]
rs1860682	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2058377	0.81[CEU][hapmap]
rs2159674	1.00[CHB][hapmap]
rs2191700	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2191701	1.00[CHB][hapmap]
rs4109977	0.82[CEU][hapmap]
rs6464754	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6464757	0.91[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.81[GIH][hapmap];0.91[TSI][hapmap]
rs6464758	0.82[CEU][hapmap]
rs6946112	1.00[CHB][hapmap]
rs6948846	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap]
rs6951145	0.81[CEU][hapmap]
rs6962126	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6963627	0.87[MEX][hapmap]
rs6969819	1.00[CHB][hapmap]
rs7780801	0.82[CEU][hapmap]
rs7788551	0.93[CHB][hapmap]
rs7800227	0.91[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap]
rs7812290	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs802194	0.82[CEU][hapmap]
rs986264	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv889384	chr7:145541783-146239545	Genic enhancers Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1020950	chr7:145683419-146264304	Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv889387	chr7:145903862-146239545	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv533345	chr7:145934546-146134958	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv933136	chr7:145995920-146076835	Enhancers Weak transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv889388	chr7:145998111-146082957	Enhancers Weak transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv524528	chr7:145998111-146086322	Enhancers Weak transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv889389	chr7:145998111-146121539	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
9	nsv934010	chr7:146006146-146076835	Enhancers Active TSS Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
10	nsv933530	chr7:146016273-146076835	Enhancers Weak transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
11	nsv608929	chr7:146020936-146082957	Enhancers Active TSS Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
12	nsv608930	chr7:146025509-146081452	Enhancers Active TSS Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1860684	TAS2R39	cis	cerebellum	SCAN
rs1860684	EPHA1	cis	parietal	SCAN

Chromatin state (count:0 , 50 per page) page:

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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