Variant report

Variant	rs12494196
Chromosome Location	chr3:85713880-85713881
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10511074	0.84[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap]
rs10511079	0.81[MEX][hapmap];0.85[TSI][hapmap]
rs11127905	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11711972	0.88[JPT][hapmap]
rs1375218	0.81[JPT][hapmap]
rs1375219	0.81[JPT][hapmap]
rs1448616	0.81[JPT][hapmap]
rs17334733	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17460638	0.81[MEX][hapmap];0.85[TSI][hapmap]
rs1947180	1.00[CEU][hapmap];0.81[JPT][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes]
rs2017676	0.93[EUR][1000 genomes]
rs2029051	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2029052	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2029053	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2044654	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2325036	0.90[JPT][hapmap]
rs2325037	0.90[JPT][hapmap]
rs4129298	0.99[EUR][1000 genomes]
rs4298053	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4302392	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap]
rs4305433	0.94[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs4312666	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4320069	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4435654	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs4482674	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4555536	0.90[JPT][hapmap]
rs4618235	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6549047	0.95[CEU][hapmap];1.00[YRI][hapmap]
rs6549048	0.99[EUR][1000 genomes]
rs6549054	0.90[JPT][hapmap]
rs6781999	1.00[CEU][hapmap];0.81[JPT][hapmap];0.99[EUR][1000 genomes]
rs6794759	0.85[TSI][hapmap]
rs6799453	0.90[JPT][hapmap]
rs73142855	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73147238	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73147239	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73147242	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7611409	0.90[JPT][hapmap]
rs7612371	0.90[JPT][hapmap]
rs7615964	0.84[CEU][hapmap];1.00[CHB][hapmap]
rs7624423	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7637221	0.81[JPT][hapmap]
rs7638774	0.90[JPT][hapmap]
rs7653470	0.90[JPT][hapmap]
rs892366	0.80[MEX][hapmap];0.85[TSI][hapmap]
rs9681744	0.89[JPT][hapmap]
rs9820133	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9820262	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9836755	0.90[JPT][hapmap]
rs9843797	0.81[CHD][hapmap];0.90[JPT][hapmap]
rs9844720	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9860249	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap]
rs9864042	0.90[JPT][hapmap]
rs9876664	0.90[JPT][hapmap]
rs9878917	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9881886	0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002238	chr3:85357855-85719373	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	1 gene(s)	inside rSNPs	diseases
2	nsv536619	chr3:85357855-85719373	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	1 gene(s)	inside rSNPs	diseases
3	nsv590905	chr3:85438564-85797093	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv1010541	chr3:85505839-85870597	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv536625	chr3:85505839-85870597	Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv877104	chr3:85646426-85737646	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:85712800-85719600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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