Variant report

Variant	rs10409531
Chromosome Location	chr19:57066013-57066014
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs10405702	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10406660	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10408033	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10410277	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10412249	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10413682	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10415256	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10419789	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10421285	1.00[CHB][hapmap];0.89[CHD][hapmap];0.90[MEX][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10424437	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10425965	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10426619	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10427145	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1052280	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11084454	1.00[CHB][hapmap];0.83[CHD][hapmap];0.90[MEX][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12104204	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12104288	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12979383	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12981572	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2024396	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28428635	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28668141	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2869896	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2904241	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4401145	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4801174	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4801335	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4801337	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4801339	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4801343	1.00[CHB][hapmap];0.83[CHD][hapmap];0.90[MEX][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7252022	1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7252934	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7253371	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7253545	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7254001	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7258886	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7259161	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7259577	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7259608	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7259741	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs741252	1.00[CHB][hapmap];0.80[CHD][hapmap];0.90[MEX][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs759331	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs764999	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs765000	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8101497	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8106879	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8108667	1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9916995	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs995934	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	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
7	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
8	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
9	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
10	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
11	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
12	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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10409531	ZFP28	Cis_1M	lymphoblastoid	RTeQTL
rs10409531	ZNF776	cis	parietal	SCAN
rs10409531	ZFP28	cis	multi-tissue	Pritchard
rs10409531	AC007228.11	cis	Esophagus Muscularis	GTEx
rs10409531	ZFP28	cis	lymphoblastoid	seeQTL

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:57047400-57077800	ZNF genes & repeats	Liver	Liver
2	chr19:57050800-57067000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr19:57051200-57068000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
4	chr19:57051400-57068000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr19:57051400-57068000	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr19:57051400-57068000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr19:57051400-57068000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr19:57051400-57070600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr19:57051600-57067200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
10	chr19:57051600-57078000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
11	chr19:57051800-57066600	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
12	chr19:57051800-57067000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
13	chr19:57052200-57070200	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
14	chr19:57052400-57068000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr19:57052600-57067800	ZNF genes & repeats	Dnd41	blood
16	chr19:57054000-57068000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr19:57054800-57077800	ZNF genes & repeats	Adipose Nuclei	Adipose
18	chr19:57055000-57067200	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
19	chr19:57055000-57070800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr19:57055200-57068000	ZNF genes & repeats	Duodenum Mucosa	Duodenum
21	chr19:57056200-57068000	ZNF genes & repeats	Brain Substantia Nigra	brain
22	chr19:57058200-57068200	ZNF genes & repeats	Colon Smooth Muscle	Colon
23	chr19:57058400-57067200	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
24	chr19:57058600-57066400	ZNF genes & repeats	Primary B cells from peripheral blood	blood
25	chr19:57058600-57068000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr19:57058800-57066800	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
27	chr19:57058800-57066800	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
28	chr19:57059000-57067800	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr19:57059200-57067400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
30	chr19:57060000-57067000	ZNF genes & repeats	Stomach Smooth Muscle	stomach
31	chr19:57060200-57066800	ZNF genes & repeats	Fetal Kidney	kidney
32	chr19:57060400-57066600	ZNF genes & repeats	NHDF-Ad	bronchial
33	chr19:57061200-57067800	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
34	chr19:57061600-57070400	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr19:57063600-57066600	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
36	chr19:57063600-57067000	ZNF genes & repeats	Brain Angular Gyrus	brain
37	chr19:57063600-57067000	ZNF genes & repeats	A549	lung
38	chr19:57063800-57067200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
39	chr19:57064000-57066600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
40	chr19:57064000-57067800	ZNF genes & repeats	Brain Germinal Matrix	brain
41	chr19:57064000-57070800	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
42	chr19:57064200-57066400	ZNF genes & repeats	Primary T cells from cord blood	blood
43	chr19:57064200-57066400	ZNF genes & repeats	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr19:57064200-57066800	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
45	chr19:57064200-57067000	ZNF genes & repeats	Fetal Lung	lung
46	chr19:57064200-57067200	ZNF genes & repeats	Primary B cells from cord blood	blood
47	chr19:57064200-57067800	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr19:57064200-57068000	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
49	chr19:57064200-57068000	ZNF genes & repeats	Brain Hippocampus Middle	brain
50	chr19:57064200-57068000	ZNF genes & repeats	Fetal Brain Female	brain

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