Variant report

Variant	rs4801950
Chromosome Location	chr19:53582131-53582132
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:53580803..53583799-chr19:53585979..53588873,2	K562	blood:
2	chr19:53580105..53582342-chr19:53607361..53608967,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000170949	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1650971	0.92[CEU][hapmap];0.85[JPT][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs167917	0.93[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs189071	0.93[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2560953	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs329696	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs329697	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs329698	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs329699	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs329700	0.93[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs329701	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];0.92[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs329702	0.93[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs329703	0.93[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs329704	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs329705	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];0.92[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs329706	0.93[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs329717	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs329718	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs329719	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];0.92[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs329738	0.93[CEU][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs329739	0.84[EUR][1000 genomes]
rs4635442	0.83[EUR][1000 genomes]
rs4801954	0.85[JPT][hapmap]
rs4803049	0.93[CEU][hapmap];0.85[JPT][hapmap];0.86[EUR][1000 genomes]
rs7253093	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7254120	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7259250	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs730192	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8100002	0.92[CEU][hapmap];0.86[CHB][hapmap];0.92[CHD][hapmap];0.81[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8111777	0.93[CEU][hapmap];0.85[JPT][hapmap];0.86[EUR][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	nsv530807	chr19:53210488-53695881	Strong transcription Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	esv3326632	chr19:53371248-53697569	Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	esv2758506	chr19:53410459-53652575	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
4	esv2758769	chr19:53410459-53652575	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
5	nsv428370	chr19:53410459-53652575	Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
6	nsv1065143	chr19:53507142-53853363	Bivalent/Poised TSS ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
7	nsv544063	chr19:53507142-53853363	ZNF genes & repeats Strong transcription Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
8	nsv1058019	chr19:53507142-53904508	ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
9	nsv544064	chr19:53507142-53904508	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
10	nsv912342	chr19:53581151-54010759	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4801950	ZNF160	cis	Thyroid	GTEx
rs4801950	ZNF160	cis	multi-tissue	Pritchard
rs4801950	ZNF160	cis	Lymphoblastoid	GTEx
rs4801950	TMEM190	cis	cerebellum	SCAN
rs4801950	ZNF160	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:53564600-53586800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
2	chr19:53564800-53586600	ZNF genes & repeats	Liver	Liver
3	chr19:53568000-53586400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr19:53568400-53588600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr19:53570200-53587400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr19:53570600-53589600	ZNF genes & repeats	GM12878-XiMat	blood
7	chr19:53571000-53587200	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
8	chr19:53571800-53583400	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
9	chr19:53571800-53586000	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
10	chr19:53571800-53586600	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
11	chr19:53573600-53604800	Weak transcription	Hela-S3	cervix
12	chr19:53574200-53584000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr19:53574600-53582400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr19:53574800-53584000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr19:53574800-53585200	Weak transcription	Psoas Muscle	Psoas
16	chr19:53574800-53599600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr19:53575600-53598600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr19:53575600-53601000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr19:53576200-53586400	ZNF genes & repeats	Duodenum Mucosa	Duodenum
20	chr19:53576400-53583200	ZNF genes & repeats	Primary T helper 17 cells PMA-I stimulated	--
21	chr19:53576800-53605200	Weak transcription	Stomach Mucosa	stomach
22	chr19:53577000-53583000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr19:53577000-53584000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr19:53577400-53587600	Weak transcription	Fetal Brain Male	brain
25	chr19:53577600-53587800	Weak transcription	NHLF	lung
26	chr19:53578200-53588600	Weak transcription	Fetal Kidney	kidney
27	chr19:53578400-53582200	ZNF genes & repeats	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr19:53578400-53583800	Weak transcription	Brain Germinal Matrix	brain
29	chr19:53578400-53587400	Weak transcription	Brain Anterior Caudate	brain
30	chr19:53578400-53588000	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr19:53578600-53585200	Weak transcription	Brain Hippocampus Middle	brain
32	chr19:53578600-53585400	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr19:53578600-53586400	Weak transcription	NH-A	brain
34	chr19:53578600-53587600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr19:53578800-53588000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr19:53578800-53593400	Weak transcription	HepG2	liver
37	chr19:53579000-53585400	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
38	chr19:53579000-53587400	Weak transcription	NHDF-Ad	bronchial
39	chr19:53579200-53582600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr19:53579200-53585200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr19:53579200-53585200	Weak transcription	Placenta	Placenta
42	chr19:53579200-53585600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr19:53579200-53585600	Weak transcription	Right Ventricle	heart
44	chr19:53579400-53584000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr19:53579400-53584200	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr19:53579400-53584800	Weak transcription	Primary hematopoietic stem cells	blood
47	chr19:53579400-53585000	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr19:53579600-53584600	Weak transcription	Stomach Smooth Muscle	stomach
49	chr19:53579800-53583000	Weak transcription	Fetal Muscle Leg	muscle
50	chr19:53580000-53583200	ZNF genes & repeats	Aorta	Aorta

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