Variant report

Variant	rs12104204
Chromosome Location	chr19:57084560-57084561
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10405702	0.86[ASN][1000 genomes]
rs10406660	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10408033	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10409531	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10410277	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10412249	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10413682	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10415256	0.86[ASN][1000 genomes]
rs10419789	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10421285	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10424437	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10425965	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10426619	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10427145	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1052280	0.87[ASN][1000 genomes]
rs11084454	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12104288	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12979383	1.00[ASN][1000 genomes]
rs12981572	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2024396	0.86[ASN][1000 genomes]
rs28428635	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28668141	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2869896	0.84[ASN][1000 genomes]
rs2904241	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4401145	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4801174	0.87[ASN][1000 genomes]
rs4801335	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4801337	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4801339	0.87[ASN][1000 genomes]
rs4801343	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7252022	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7252934	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7253371	0.86[ASN][1000 genomes]
rs7253545	0.86[ASN][1000 genomes]
rs7254001	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7258886	0.87[ASN][1000 genomes]
rs7259161	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7259577	0.87[ASN][1000 genomes]
rs7259608	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7259741	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs741252	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs759331	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs764999	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs765000	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs8101497	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs8106879	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs8108667	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9916995	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs995934	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	nsv912518	chr19:56995737-57109821	Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
10	nsv1062806	chr19:57050734-57191914	ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12104204	ZFP28	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:57079200-57090000	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr19:57079200-57090200	ZNF genes & repeats	Dnd41	blood
3	chr19:57079200-57093400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr19:57079400-57086800	ZNF genes & repeats	Primary B cells from peripheral blood	blood
5	chr19:57079400-57092800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr19:57079600-57084600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr19:57079600-57086600	ZNF genes & repeats	NH-A	brain
8	chr19:57079600-57088800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
9	chr19:57079600-57089400	ZNF genes & repeats	Primary B cells from cord blood	blood
10	chr19:57079600-57090200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr19:57079600-57090200	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
12	chr19:57079600-57090400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
13	chr19:57079600-57094200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr19:57079600-57094400	ZNF genes & repeats	Duodenum Mucosa	Duodenum
15	chr19:57079600-57095600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
16	chr19:57079800-57089200	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr19:57079800-57089400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr19:57079800-57090000	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
19	chr19:57079800-57090800	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr19:57079800-57091000	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
21	chr19:57079800-57091800	ZNF genes & repeats	Fetal Lung	lung
22	chr19:57079800-57091800	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
23	chr19:57079800-57092000	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
24	chr19:57079800-57092400	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
25	chr19:57079800-57093600	ZNF genes & repeats	Primary T cells from cord blood	blood
26	chr19:57079800-57094400	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr19:57079800-57094600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr19:57079800-57095400	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
29	chr19:57079800-57096000	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr19:57079800-57096200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr19:57079800-57096200	ZNF genes & repeats	Adipose Nuclei	Adipose
32	chr19:57079800-57100000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
33	chr19:57079800-57101800	ZNF genes & repeats	Liver	Liver
34	chr19:57080000-57088400	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
35	chr19:57080000-57088400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr19:57080000-57090200	ZNF genes & repeats	Fetal Muscle Leg	muscle
37	chr19:57080000-57090400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
38	chr19:57080000-57091200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
39	chr19:57080000-57092200	ZNF genes & repeats	Colon Smooth Muscle	Colon
40	chr19:57080000-57094600	ZNF genes & repeats	Brain Anterior Caudate	brain
41	chr19:57080000-57094800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr19:57080200-57086400	ZNF genes & repeats	Brain Hippocampus Middle	brain
43	chr19:57080200-57089800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr19:57080400-57089800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
45	chr19:57080400-57090000	ZNF genes & repeats	Stomach Smooth Muscle	stomach
46	chr19:57080400-57090800	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
47	chr19:57080400-57091800	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
48	chr19:57080400-57094600	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
49	chr19:57080600-57089800	ZNF genes & repeats	Fetal Muscle Trunk	muscle
50	chr19:57080600-57091600	ZNF genes & repeats	Psoas Muscle	Psoas

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