Variant report

Variant	rs11172840
Chromosome Location	chr12:59350573-59350574
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10877188	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10877198	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10877200	0.93[EUR][1000 genomes]
rs11172823	0.82[EUR][1000 genomes]
rs11172824	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs11172825	0.82[EUR][1000 genomes]
rs11172827	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11172831	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11172833	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11172837	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172839	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172846	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172857	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11172858	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11172860	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11172861	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11172862	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11172866	0.93[EUR][1000 genomes]
rs11172867	0.93[EUR][1000 genomes]
rs11172868	0.96[EUR][1000 genomes]
rs11172869	0.84[EUR][1000 genomes]
rs11172870	0.86[EUR][1000 genomes]
rs12368752	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12369750	0.82[EUR][1000 genomes]
rs12370522	0.83[AMR][1000 genomes]
rs12423502	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12424788	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12426212	0.81[EUR][1000 genomes]
rs12426969	0.82[EUR][1000 genomes]
rs17121828	0.93[EUR][1000 genomes]
rs55888651	0.93[EUR][1000 genomes]
rs58692617	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs60522760	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60984323	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61754220	0.82[EUR][1000 genomes]
rs61919461	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61919462	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61919464	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61919465	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61919466	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61919469	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61919471	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61919513	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61919518	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61919519	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61919520	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61919521	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61919523	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61919524	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61919525	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61919531	0.97[EUR][1000 genomes]
rs61919532	0.97[EUR][1000 genomes]
rs6581224	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7136193	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7138401	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7294684	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7297094	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7301299	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7302365	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7303773	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7309872	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7963207	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7968111	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7969722	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7970054	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7980136	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7980483	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9645802	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][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	nsv1043385	chr12:59149582-59758952	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv1067596	chr12:59167152-59764208	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv492251	chr12:59167152-59764208	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv559048	chr12:59336737-59440659	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:59344600-59355000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr12:59345000-59354000	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr12:59346600-59354000	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr12:59348600-59352600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr12:59349600-59351200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr12:59349600-59351200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr12:59349800-59351200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr12:59349800-59351400	Enhancers	iPS-18 Cell Line	embryonic stem cell
9	chr12:59350000-59351400	Enhancers	iPS-20b Cell Line	embryonic stem cell
10	chr12:59350200-59354400	Weak transcription	Duodenum Mucosa	Duodenum
11	chr12:59350400-59350800	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr12:59350400-59351000	Weak transcription	HUES64 Cell Line	embryonic stem cell

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