Variant report

Variant	rs11111940
Chromosome Location	chr12:104628831-104628832
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10778321	0.86[JPT][hapmap]
rs10861169	0.81[YRI][hapmap]
rs10861171	0.84[YRI][hapmap]
rs10861176	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10861179	0.83[ASN][1000 genomes]
rs10861185	0.86[JPT][hapmap]
rs10861187	0.86[JPT][hapmap]
rs10861197	0.86[JPT][hapmap]
rs11111916	0.89[CHD][hapmap];0.90[JPT][hapmap]
rs11111917	0.89[CHD][hapmap];0.90[JPT][hapmap]
rs11111938	0.82[JPT][hapmap]
rs11111979	0.86[JPT][hapmap]
rs11111980	0.86[JPT][hapmap]
rs11111987	0.86[JPT][hapmap]
rs11836726	0.89[CHD][hapmap];0.90[JPT][hapmap]
rs12305190	0.87[MKK][hapmap]
rs17202060	0.86[JPT][hapmap]
rs4246260	0.87[CEU][hapmap];0.94[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap];0.83[EUR][1000 genomes]
rs4246261	0.83[EUR][1000 genomes]
rs4246263	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4246265	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4321026	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4371000	0.81[EUR][1000 genomes]
rs4445711	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4592489	0.81[ASN][1000 genomes]
rs4595619	0.86[JPT][hapmap]
rs4609668	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4964256	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4964626	0.83[EUR][1000 genomes]
rs4964628	0.87[CEU][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];0.83[EUR][1000 genomes]
rs4964678	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4964782	0.86[JPT][hapmap]
rs5005907	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5018287	0.86[JPT][hapmap]
rs6539130	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7294778	0.86[JPT][hapmap]
rs7297296	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7297956	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7397748	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7488680	0.86[JPT][hapmap]
rs7954970	0.81[JPT][hapmap]
rs7957744	0.87[CEU][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes]
rs7958262	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs7961381	0.81[EUR][1000 genomes]
rs7966970	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7969538	0.83[EUR][1000 genomes]
rs7972172	0.86[CHD][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];0.83[EUR][1000 genomes]
rs7975524	1.00[CEU][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]

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	esv1842062	chr12:104531180-104638773	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	n/a
2	nsv899493	chr12:104548613-104703228	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv899494	chr12:104561521-104806232	Flanking Active TSS Weak transcription Genic enhancers Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv1046606	chr12:104606617-104763734	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv1038609	chr12:104613847-104764981	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	nsv541587	chr12:104613847-104764981	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11111940	EID3	cis	Adipose Subcutaneous	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104628400-104629600	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell

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