Variant report

Variant	rs10406795
Chromosome Location	chr19:52913417-52913418
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	chr19:52901728..52903647-chr19:52912630..52914410,2	MCF-7	breast:

Extended variants
information (count: 18 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11666879	0.84[EUR][1000 genomes]
rs11670607	0.82[CEU][hapmap]
rs11672854	0.82[CEU][hapmap];0.82[CHB][hapmap];0.81[EUR][1000 genomes]
rs17836094	0.81[EUR][1000 genomes]
rs2290747	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56778898	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs60807333	0.82[AMR][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	nsv833873	chr19:52788939-52937281	Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv1066537	chr19:52794424-53044977	Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv544060	chr19:52794424-53044977	ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	nsv912300	chr19:52832830-52928039	Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv912301	chr19:52835210-52914233	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv912302	chr19:52859828-52928039	Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
7	nsv912303	chr19:52874140-52928039	ZNF genes & repeats Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	nsv521079	chr19:52886137-52917626	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	nsv828615	chr19:52888767-52936555	ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
10	esv2762048	chr19:52895166-52997571	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
11	esv3412133	chr19:52907745-52935907	ZNF genes & repeats Weak transcription Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs10406795	ZNF534	cis	Skin Sun Exposed Lower leg	GTEx
rs10406795	ZNF534	cis	Adipose Subcutaneous	GTEx
rs10406795	ZNF528	cis	Nerve Tibial	GTEx
rs10406795	ZNF534	cis	Nerve Tibial	GTEx
rs10406795	ZNF534	cis	Muscle Skeletal	GTEx
rs10406795	ZNF534	cis	Thyroid	GTEx
rs10406795	ZNF534	cis	Artery Tibial	GTEx
rs10406795	ZNF534	cis	lung	GTEx

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52902000-52913800	Weak transcription	Fetal Heart	heart
2	chr19:52902200-52913800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr19:52902200-52917400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr19:52902200-52919200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr19:52902400-52917600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr19:52902600-52913600	Strong transcription	Stomach Smooth Muscle	stomach
7	chr19:52902600-52914000	ZNF genes & repeats	Lung	lung
8	chr19:52902600-52917600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr19:52902600-52918200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
10	chr19:52902800-52914000	Strong transcription	Cortex derived primary cultured neurospheres	brain
11	chr19:52902800-52914200	Strong transcription	Brain Anterior Caudate	brain
12	chr19:52902800-52914200	Strong transcription	Skeletal Muscle Female	skeletal muscle
13	chr19:52902800-52915600	Strong transcription	HSMMtube	muscle
14	chr19:52902800-52924200	ZNF genes & repeats	Liver	Liver
15	chr19:52903000-52913600	Strong transcription	Brain Cingulate Gyrus	brain
16	chr19:52903000-52913600	Strong transcription	Brain Hippocampus Middle	brain
17	chr19:52903000-52914000	ZNF genes & repeats	Ovary	ovary
18	chr19:52903000-52916200	Strong transcription	Skeletal Muscle Male	skeletal muscle
19	chr19:52903200-52916800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
20	chr19:52904200-52914000	ZNF genes & repeats	Fetal Intestine Small	intestine
21	chr19:52904200-52917200	Strong transcription	Brain Germinal Matrix	brain
22	chr19:52904200-52917600	Strong transcription	Right Ventricle	heart
23	chr19:52904400-52916200	Strong transcription	Muscle Satellite Cultured Cells	--
24	chr19:52904400-52916200	Strong transcription	Brain Angular Gyrus	brain
25	chr19:52904400-52916600	Strong transcription	Placenta Amnion	Placenta Amnion
26	chr19:52905000-52916000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
27	chr19:52905000-52916800	ZNF genes & repeats	Spleen	Spleen
28	chr19:52905000-52920800	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr19:52905000-52923800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
30	chr19:52905200-52913800	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
31	chr19:52905200-52917800	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr19:52905400-52914000	ZNF genes & repeats	Pancreas	Pancrea
33	chr19:52905400-52915600	Strong transcription	Osteobl	bone
34	chr19:52906400-52916000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr19:52906400-52920600	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
36	chr19:52906600-52921000	ZNF genes & repeats	Duodenum Mucosa	Duodenum
37	chr19:52906800-52916200	Weak transcription	NHLF	lung
38	chr19:52907000-52915600	ZNF genes & repeats	Primary B cells from peripheral blood	blood
39	chr19:52907200-52914400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr19:52907400-52918000	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
41	chr19:52907400-52919000	ZNF genes & repeats	Aorta	Aorta
42	chr19:52908200-52919400	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr19:52908400-52915200	ZNF genes & repeats	Small Intestine	intestine
44	chr19:52908400-52915600	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
45	chr19:52908600-52915800	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
46	chr19:52908600-52917000	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
47	chr19:52908600-52920800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr19:52909200-52913800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr19:52909200-52915000	ZNF genes & repeats	Placenta	Placenta
50	chr19:52909400-52914400	Strong transcription	Primary T helper naive cells from peripheral blood	blood

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