Variant report

Variant	rs4405390
Chromosome Location	chr12:40139756-40139757
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 130 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:123)

rs_ID	r²[population]
rs10047563	0.87[AMR][1000 genomes]
rs10219652	0.93[CEU][hapmap];0.89[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10444570	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10735885	0.94[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10747825	0.89[JPT][hapmap]
rs10747853	0.80[EUR][1000 genomes]
rs10747877	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10747878	0.93[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10783959	0.94[CEU][hapmap]
rs10783969	0.83[JPT][hapmap]
rs10783993	0.89[AMR][1000 genomes]
rs10783994	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10783998	0.87[AMR][1000 genomes]
rs10784001	0.89[JPT][hapmap];0.89[AMR][1000 genomes]
rs10784016	0.89[JPT][hapmap];0.87[AMR][1000 genomes]
rs10784019	0.89[JPT][hapmap]
rs10784034	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10784051	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10784059	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10784065	0.83[CEU][hapmap]
rs10877335	0.87[AMR][1000 genomes]
rs10877337	0.91[AMR][1000 genomes]
rs10877369	0.84[AMR][1000 genomes]
rs10877383	0.93[CEU][hapmap];0.89[JPT][hapmap]
rs10877410	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11173013	0.89[JPT][hapmap]
rs11173257	0.82[AMR][1000 genomes]
rs11173259	0.91[EUR][1000 genomes]
rs11173260	0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11173262	0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11173376	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11173394	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11173401	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11173411	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11173423	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11173424	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11173428	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11173433	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11173434	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11173440	0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11173446	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11173459	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11173494	0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11173507	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11173541	0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11173550	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11173551	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11173553	0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11532458	0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12229203	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12229301	0.89[JPT][hapmap]
rs12229418	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12230687	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12299938	0.86[ASN][1000 genomes]
rs12823801	0.94[CEU][hapmap];0.89[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12825223	0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4077987	0.89[JPT][hapmap]
rs4238072	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4238073	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4255599	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4255600	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4312128	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4322460	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4322461	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4337105	0.89[JPT][hapmap]
rs4357762	0.89[JPT][hapmap]
rs4381428	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4388963	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4391875	0.83[ASN][1000 genomes]
rs4397916	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4405391	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4411336	0.93[CEU][hapmap];0.89[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4417381	0.82[CEU][hapmap];0.88[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4417382	0.89[JPT][hapmap];0.89[AMR][1000 genomes]
rs4495951	0.89[JPT][hapmap]
rs4556618	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4594067	0.89[JPT][hapmap];0.89[AMR][1000 genomes]
rs4767949	0.87[CEU][hapmap];0.84[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4768168	0.89[JPT][hapmap];0.89[AMR][1000 genomes]
rs4768169	0.89[JPT][hapmap];0.87[AMR][1000 genomes]
rs4768170	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57244766	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs58418587	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs58755301	0.85[AMR][1000 genomes]
rs61477638	0.82[ASN][1000 genomes]
rs61931185	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61931208	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61931211	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs61933102	0.87[AMR][1000 genomes]
rs61933154	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61933157	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61933158	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6421195	0.87[AMR][1000 genomes]
rs6421196	0.89[JPT][hapmap];0.87[AMR][1000 genomes]
rs6421197	0.87[AMR][1000 genomes]
rs6421198	0.89[AMR][1000 genomes]
rs6581250	0.94[CEU][hapmap];0.89[JPT][hapmap]
rs6581263	0.83[JPT][hapmap];0.87[AMR][1000 genomes]
rs6581265	0.89[AMR][1000 genomes]
rs6581266	0.89[AMR][1000 genomes]
rs6581270	0.87[AMR][1000 genomes]
rs6581271	0.89[JPT][hapmap];0.87[AMR][1000 genomes]
rs6581272	0.89[AMR][1000 genomes]
rs6581294	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7136929	0.87[AMR][1000 genomes]
rs7296585	0.87[AMR][1000 genomes]
rs7298453	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7301886	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7302849	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7308955	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7485345	0.83[JPT][hapmap];0.87[AMR][1000 genomes]
rs7486196	0.89[AMR][1000 genomes]
rs7486621	0.87[AMR][1000 genomes]
rs7487812	0.93[CEU][hapmap]
rs7487999	0.89[JPT][hapmap]
rs7952735	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7956577	0.87[AMR][1000 genomes]
rs7959905	0.87[AMR][1000 genomes]
rs7961070	0.89[AMR][1000 genomes]
rs7961346	0.89[JPT][hapmap]
rs7964129	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7969282	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7980636	0.89[JPT][hapmap]

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	nsv531527	chr12:39680812-40182822	Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv1037457	chr12:39898349-40245401	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv541480	chr12:39898349-40245401	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv899024	chr12:40046408-40188870	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv1053603	chr12:40082673-40197609	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv427907	chr12:40122713-40199621	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv428280	chr12:40122713-40199621	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40130800-40156400	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr12:40137200-40145800	Weak transcription	Aorta	Aorta
3	chr12:40137200-40154200	Weak transcription	Liver	Liver

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