Variant report

Variant	rs12981894
Chromosome Location	chr19:53723679-53723680
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:53722523..53724411-chr19:53731343..53734094,2	K562	blood:

Extended variants
information (count: 67 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10401578	0.82[CHB][hapmap];0.80[CHD][hapmap]
rs10404048	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.85[GIH][hapmap];0.81[JPT][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10413453	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10417666	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11084227	0.82[CHB][hapmap];0.81[CHD][hapmap]
rs1129002	0.87[CHB][hapmap]
rs12984188	0.87[CHB][hapmap]
rs12984473	0.87[CHB][hapmap]
rs17272966	0.87[CHB][hapmap]
rs2914371	0.82[CHB][hapmap]
rs2914372	0.80[CHB][hapmap]
rs2914373	0.89[ASN][1000 genomes]
rs2914374	0.89[ASN][1000 genomes]
rs2914376	0.87[CHB][hapmap]
rs2914378	0.87[CHB][hapmap]
rs2914379	0.89[ASN][1000 genomes]
rs2914381	1.00[CHB][hapmap];0.81[JPT][hapmap];0.89[ASN][1000 genomes]
rs2914382	0.89[ASN][1000 genomes]
rs2914383	0.82[CHB][hapmap]
rs2965221	1.00[CHB][hapmap];0.81[JPT][hapmap];0.83[YRI][hapmap];0.89[ASN][1000 genomes]
rs2965223	1.00[CHB][hapmap];0.81[JPT][hapmap];0.89[ASN][1000 genomes]
rs2965224	1.00[CHB][hapmap];0.91[CHD][hapmap];0.81[JPT][hapmap];0.89[ASN][1000 genomes]
rs2965225	0.89[ASN][1000 genomes]
rs2965226	0.89[ASN][1000 genomes]
rs2965227	0.89[ASN][1000 genomes]
rs2965228	0.91[ASW][hapmap];0.91[YRI][hapmap]
rs2965230	1.00[CHB][hapmap];0.86[JPT][hapmap];0.80[YRI][hapmap];0.89[ASN][1000 genomes]
rs2965231	1.00[CHB][hapmap];0.81[JPT][hapmap];0.82[YRI][hapmap];0.89[ASN][1000 genomes]
rs2965232	0.89[ASN][1000 genomes]
rs2965233	0.89[ASN][1000 genomes]
rs2965234	0.89[ASN][1000 genomes]
rs2965235	0.89[ASN][1000 genomes]
rs2965239	0.89[ASN][1000 genomes]
rs2965241	0.88[ASN][1000 genomes]
rs2965242	0.80[CHB][hapmap]
rs3097251	0.89[ASN][1000 genomes]
rs3111318	0.87[ASN][1000 genomes]
rs3111320	0.89[ASN][1000 genomes]
rs4239497	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4801972	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4803068	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4803070	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4803077	0.86[ASN][1000 genomes]
rs55852652	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6509736	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7247982	0.90[ASW][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];0.88[JPT][hapmap];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7248561	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7248781	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7248812	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7248883	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7249931	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7253646	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7257238	0.82[ASN][1000 genomes]
rs8104393	0.89[ASN][1000 genomes]
rs8104750	0.89[ASN][1000 genomes]
rs8105607	0.87[ASN][1000 genomes]
rs8109793	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9788	0.90[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];0.88[JPT][hapmap];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065143	chr19:53507142-53853363	Bivalent/Poised TSS ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv544063	chr19:53507142-53853363	ZNF genes & repeats Strong transcription Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
3	nsv1058019	chr19:53507142-53904508	ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
4	nsv544064	chr19:53507142-53904508	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
5	nsv912342	chr19:53581151-54010759	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	nsv1063630	chr19:53591444-54419183	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	282 gene(s)	inside rSNPs	diseases
7	nsv1055378	chr19:53603268-53951855	Flanking Bivalent TSS/Enh Enhancers Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
8	nsv544065	chr19:53603268-53951855	Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
9	esv2830362	chr19:53681132-53933147	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12981894	ZNF17	cis	cerebellum	SCAN
rs12981894	ZNF547	cis	cerebellum	SCAN
rs12981894	CPD	trans	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:53701600-53724800	ZNF genes & repeats	Liver	Liver
2	chr19:53701600-53725000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
3	chr19:53701600-53725000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
4	chr19:53701800-53725400	ZNF genes & repeats	Adipose Nuclei	Adipose
5	chr19:53702400-53724800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr19:53721600-53724200	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
7	chr19:53722800-53724600	ZNF genes & repeats	Brain Anterior Caudate	brain

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