Variant report

Variant	rs11173541
Chromosome Location	chr12:40173704-40173705
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 131 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:124)

rs_ID	r²[population]
rs10047563	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10219652	0.84[JPT][hapmap];0.83[AMR][1000 genomes]
rs10444570	0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10735885	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10747825	1.00[CEU][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs10747877	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10747878	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10783969	1.00[CEU][hapmap]
rs10783993	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10783994	0.81[AMR][1000 genomes]
rs10783998	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10784001	1.00[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10784016	1.00[CEU][hapmap];0.84[JPT][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10784019	1.00[CEU][hapmap];0.83[JPT][hapmap]
rs10784034	0.83[AMR][1000 genomes]
rs10784051	0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10784059	0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10877335	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10877337	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10877369	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10877383	0.84[JPT][hapmap]
rs10877410	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11172998	0.83[EUR][1000 genomes]
rs11173013	1.00[CEU][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap]
rs11173257	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11173260	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11173262	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11173376	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11173394	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11173401	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11173411	0.92[ASN][1000 genomes]
rs11173423	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11173424	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11173428	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11173433	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11173434	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11173440	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11173446	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11173459	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11173494	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11173507	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11173550	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11173551	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11173553	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11532458	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12229203	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12229301	1.00[CEU][hapmap];0.84[JPT][hapmap]
rs12229418	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12230687	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12299938	0.82[ASN][1000 genomes]
rs12823801	0.84[JPT][hapmap];0.83[AMR][1000 genomes]
rs12825223	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4077987	0.90[CEU][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap]
rs4129365	1.00[CEU][hapmap]
rs4238072	0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4238073	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4255599	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4255600	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4312128	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4322460	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4322461	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4337105	1.00[CEU][hapmap];0.84[JPT][hapmap]
rs4357762	1.00[CEU][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap]
rs4381428	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4388963	0.83[AMR][1000 genomes]
rs4391875	0.89[ASN][1000 genomes]
rs4397916	0.90[ASN][1000 genomes]
rs4405390	0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4405391	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4411336	0.84[JPT][hapmap]
rs4417381	0.82[JPT][hapmap];0.83[AMR][1000 genomes]
rs4417382	1.00[CEU][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4495951	1.00[CEU][hapmap];0.84[JPT][hapmap]
rs4556618	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4594067	1.00[CEU][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4767949	0.83[AMR][1000 genomes]
rs4768166	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs4768168	0.91[CEU][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4768169	0.91[CEU][hapmap];0.84[JPT][hapmap];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4768170	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs57244766	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs58418587	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs58755301	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61931185	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61931208	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61931211	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61933102	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61933154	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61933157	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61933158	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6421191	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs6421195	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6421196	1.00[CEU][hapmap];0.84[JPT][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6421197	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6421198	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6581250	0.84[JPT][hapmap]
rs6581263	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6581265	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6581266	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6581270	0.90[CEU][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6581271	1.00[CEU][hapmap];0.84[JPT][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6581272	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6581294	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7136929	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7296585	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7298453	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7301886	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7302849	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7308955	0.81[AMR][1000 genomes]
rs7485345	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7486196	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7486621	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7486631	0.83[JPT][hapmap]
rs7487999	1.00[CEU][hapmap];0.84[JPT][hapmap]
rs7952735	0.83[AMR][1000 genomes]
rs7956577	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7959905	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7961070	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7961346	1.00[CEU][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs7964129	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7969282	0.91[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7973312	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs7980636	1.00[CEU][hapmap];0.83[JPT][hapmap];0.83[EUR][1000 genomes]
rs9325166	0.91[CEU][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:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40145000-40175000	Weak transcription	Right Ventricle	heart
2	chr12:40158200-40174400	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr12:40158200-40179000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr12:40158200-40199000	Weak transcription	Left Ventricle	heart
5	chr12:40161600-40198800	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr12:40171600-40175000	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr12:40172600-40174800	Enhancers	Hela-S3	cervix
8	chr12:40172800-40174400	Enhancers	Colon Smooth Muscle	Colon
9	chr12:40173000-40175600	Enhancers	Rectal Smooth Muscle	rectum

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