Variant report

Variant	rs10423274
Chromosome Location	chr19:56979877-56979878
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:56978548..56980333-chr19:56983464..56985765,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF582-2	chr19:56979088-56980304	ENSG00000250660

Variant related genes	Relation type
ENSG00000198046	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10404523	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10408921	0.93[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.90[MEX][hapmap];0.97[MKK][hapmap];0.96[TSI][hapmap];0.80[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10410530	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.90[MEX][hapmap];0.81[TSI][hapmap];0.92[ASN][1000 genomes]
rs10413986	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12462739	0.81[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.85[JPT][hapmap];0.88[TSI][hapmap]
rs3760848	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.96[TSI][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4801321	0.81[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.85[JPT][hapmap];0.88[TSI][hapmap]
rs4801322	0.81[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.85[JPT][hapmap];0.88[TSI][hapmap];0.83[ASN][1000 genomes]
rs60732696	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66718632	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7258501	0.81[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.85[JPT][hapmap];0.88[TSI][hapmap];0.83[ASN][1000 genomes]
rs8112950	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912516	chr19:56601298-56981382	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	93 gene(s)	inside rSNPs	diseases
2	nsv949121	chr19:56754719-57591038	ZNF genes & repeats Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
3	nsv1062341	chr19:56794070-57273332	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
4	nsv544094	chr19:56794070-57273332	Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
5	nsv1056713	chr19:56799151-57265682	ZNF genes & repeats Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
6	nsv544095	chr19:56799151-57265682	Strong transcription ZNF genes & repeats Active TSS Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
7	nsv580385	chr19:56918598-57072433	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
8	nsv1057240	chr19:56919831-57153659	Flanking Active TSS Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
9	nsv544097	chr19:56919831-57153659	Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
10	nsv580386	chr19:56924761-57072433	Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
11	nsv1055357	chr19:56933632-57190007	ZNF genes & repeats Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10423274	ZNF667	cis	Nerve Tibial	GTEx
rs10423274	ZNF460	cis	parietal	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56957200-56987400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr19:56957400-56985000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
3	chr19:56957400-56987400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
4	chr19:56957400-56987400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr19:56967200-56987600	Weak transcription	Fetal Heart	heart
6	chr19:56969400-56987600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr19:56970200-56981400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr19:56972800-56987600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr19:56973000-56981400	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr19:56973000-56981600	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr19:56973200-56981000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr19:56973400-56981600	Weak transcription	Psoas Muscle	Psoas
13	chr19:56973400-56983600	Weak transcription	Dnd41	blood
14	chr19:56973600-56981800	Weak transcription	Left Ventricle	heart
15	chr19:56974000-56981000	Weak transcription	Fetal Muscle Trunk	muscle
16	chr19:56974000-56981400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr19:56974000-56981600	Weak transcription	Right Ventricle	heart
18	chr19:56975600-56985200	ZNF genes & repeats	Brain Germinal Matrix	brain
19	chr19:56975600-56987200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr19:56976800-56987200	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr19:56977000-56980000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
22	chr19:56977400-56981400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr19:56977600-56981000	Weak transcription	Brain Anterior Caudate	brain
24	chr19:56978000-56984400	ZNF genes & repeats	Adipose Nuclei	Adipose
25	chr19:56978600-56981400	Weak transcription	HSMMtube	muscle
26	chr19:56979400-56982600	ZNF genes & repeats	Fetal Brain Male	brain
27	chr19:56979600-56980000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr19:56979800-56981400	Weak transcription	Brain Angular Gyrus	brain
29	chr19:56979800-56981800	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
30	chr19:56979800-56985000	ZNF genes & repeats	Brain Cingulate Gyrus	brain

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