Variant report

Variant	rs12972381
Chromosome Location	chr19:56880744-56880745
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:56832521..56834727-chr19:56879587..56882084,2	K562	blood:
2	chr19:56878151..56881655-chr19:56903333..56906269,7	K562	blood:
3	chr19:56878056..56881655-chr19:56903333..56906269,5	K562	blood:
4	chr19:56826282..56828501-chr19:56879622..56881209,2	K562	blood:

Variant related genes	Relation type
ENSG00000267549	Chromatin interaction
ENSG00000267454	Chromatin interaction
ENSG00000200646	Chromatin interaction
ENSG00000266907	Chromatin interaction
ENSG00000131848	Chromatin interaction
ENSG00000018869	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs36029922	0.82[EUR][1000 genomes]
rs62122530	1.00[AFR][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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12972381	ZNF542	cis	multi-tissue	Pritchard

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56878800-56880800	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr19:56879000-56880800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr19:56879000-56880800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr19:56879000-56880800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr19:56879000-56880800	Active TSS	HepG2	liver
6	chr19:56879000-56880800	Active TSS	HSMMtube	muscle
7	chr19:56879000-56880800	Active TSS	NHDF-Ad	bronchial
8	chr19:56879000-56881000	Active TSS	H9 Cell Line	embryonic stem cell
9	chr19:56879000-56881000	Active TSS	HUES6 Cell Line	embryonic stem cell
10	chr19:56879000-56881000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr19:56879000-56881000	Active TSS	Psoas Muscle	Psoas
12	chr19:56879000-56881200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr19:56879200-56880800	Active TSS	Stomach Mucosa	stomach
14	chr19:56879200-56880800	ZNF genes & repeats	GM12878-XiMat	blood
15	chr19:56879200-56880800	Active TSS	HMEC	breast
16	chr19:56879200-56881000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr19:56879200-56881000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr19:56879200-56881000	Active TSS	NHLF	lung
19	chr19:56879600-56880800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr19:56879600-56880800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
21	chr19:56879800-56880800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
22	chr19:56879800-56880800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr19:56879800-56881000	Flanking Active TSS	Primary hematopoietic stem cells	blood
24	chr19:56879800-56882200	ZNF genes & repeats	A549	lung
25	chr19:56880000-56880800	Flanking Active TSS	Primary T cells from cord blood	blood
26	chr19:56880000-56880800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
27	chr19:56880000-56880800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
28	chr19:56880000-56880800	Flanking Active TSS	Stomach Smooth Muscle	stomach
29	chr19:56880000-56880800	Flanking Active TSS	NH-A	brain
30	chr19:56880000-56881000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
31	chr19:56880000-56881000	Flanking Active TSS	Adipose Nuclei	Adipose
32	chr19:56880000-56881000	Flanking Active TSS	Brain Angular Gyrus	brain
33	chr19:56880000-56881000	Enhancers	Spleen	Spleen
34	chr19:56880200-56880800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
35	chr19:56880200-56880800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr19:56880200-56880800	Flanking Active TSS	Brain Cingulate Gyrus	brain
37	chr19:56880200-56880800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
38	chr19:56880200-56880800	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
39	chr19:56880200-56880800	Flanking Active TSS	Duodenum Mucosa	Duodenum
40	chr19:56880200-56880800	Enhancers	Gastric	stomach
41	chr19:56880200-56880800	Flanking Active TSS	Rectal Smooth Muscle	rectum
42	chr19:56880200-56880800	Flanking Active TSS	Right Atrium	heart
43	chr19:56880200-56880800	Flanking Active TSS	Thymus	Thymus
44	chr19:56880200-56881000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr19:56880200-56881000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
46	chr19:56880200-56881000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr19:56880200-56881000	Flanking Active TSS	Brain Anterior Caudate	brain
48	chr19:56880200-56881000	Flanking Active TSS	Brain Substantia Nigra	brain
49	chr19:56880200-56881000	Flanking Active TSS	Colon Smooth Muscle	Colon
50	chr19:56880200-56881000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum

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