Variant report

Variant	rs10860990
Chromosome Location	chr12:103765744-103765745
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10778228	0.86[CEU][hapmap];0.91[TSI][hapmap]
rs10778231	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs10778232	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10778236	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10778237	1.00[ASW][hapmap];0.95[CEU][hapmap];0.85[GIH][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10778238	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10860977	0.86[CEU][hapmap];0.91[TSI][hapmap];0.80[EUR][1000 genomes]
rs11111539	0.82[CEU][hapmap]
rs11111540	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12301542	0.95[CEU][hapmap]
rs1343868	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1879621	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1996749	0.86[CEU][hapmap];0.80[CHB][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs2374052	0.95[CEU][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2374060	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2374061	0.91[CEU][hapmap];0.85[TSI][hapmap];0.92[EUR][1000 genomes]
rs4764732	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4764949	0.86[CEU][hapmap];0.89[TSI][hapmap]
rs4764952	0.85[EUR][1000 genomes]
rs4764955	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6539066	0.90[CEU][hapmap];0.85[EUR][1000 genomes]
rs6539069	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6539070	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6539071	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7137989	0.86[CEU][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs7306825	0.87[CEU][hapmap]
rs7316140	0.82[CEU][hapmap]
rs7969597	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7970479	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7970531	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7971321	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs8181626	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]

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	nsv455703	chr12:103692799-103818049	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
2	nsv560037	chr12:103692799-103818049	Enhancers Bivalent Enhancer Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
3	nsv899477	chr12:103747515-103817326	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	nsv899478	chr12:103747515-103834275	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10860990	EID3	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:103707200-103786400	Weak transcription	Primary B cells from cord blood	blood
2	chr12:103760400-103766400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr12:103763600-103786400	Weak transcription	Primary B cells from peripheral blood	blood
4	chr12:103765600-103766400	Enhancers	Primary T helper naive cells fromperipheralblood	blood

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