Variant report

Variant	rs2560953
Chromosome Location	chr19:53587969-53587970
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:53577559..53580401-chr19:53586109..53588069,3	K562	blood:

Variant related genes	Relation type
ENSG00000170949	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs1650971	1.00[CEU][hapmap];0.92[JPT][hapmap];0.87[EUR][1000 genomes]
rs167917	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs189071	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs329696	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs329697	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs329698	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs329699	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs329700	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs329701	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs329702	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs329703	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs329704	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs329705	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs329706	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs329717	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs329718	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs329719	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs329738	1.00[CEU][hapmap];0.84[JPT][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs329739	0.84[EUR][1000 genomes]
rs4635442	0.83[EUR][1000 genomes]
rs4801950	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]
rs4801954	0.92[JPT][hapmap]
rs4803049	1.00[CEU][hapmap];0.92[JPT][hapmap];0.86[EUR][1000 genomes]
rs7253093	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7254120	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7259250	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs730192	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8100002	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8111777	1.00[CEU][hapmap];0.92[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2560953	TMEM190	cis	cerebellum	SCAN
rs2560953	LOC91664	cis	multi-tissue	Pritchard
rs2560953	ZNF160	cis	multi-tissue	Pritchard
rs2560953	ZNF160	cis	Adipose Subcutaneous	GTEx
rs2560953	ZNF160	cis	Thyroid	GTEx
rs2560953	ZNF160	cis	Lymphoblastoid	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:53568400-53588600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr19:53570600-53589600	ZNF genes & repeats	GM12878-XiMat	blood
3	chr19:53573600-53604800	Weak transcription	Hela-S3	cervix
4	chr19:53574800-53599600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr19:53575600-53598600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr19:53575600-53601000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr19:53576800-53605200	Weak transcription	Stomach Mucosa	stomach
8	chr19:53578200-53588600	Weak transcription	Fetal Kidney	kidney
9	chr19:53578400-53588000	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr19:53578800-53588000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr19:53578800-53593400	Weak transcription	HepG2	liver
12	chr19:53580400-53588000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr19:53580600-53588000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr19:53580600-53588800	Weak transcription	Colon Smooth Muscle	Colon
15	chr19:53580600-53589000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr19:53580600-53597800	Weak transcription	Fetal Heart	heart
17	chr19:53581000-53591200	Strong transcription	Fetal Intestine Large	intestine
18	chr19:53582400-53588000	Weak transcription	Brain Substantia Nigra	brain
19	chr19:53583800-53588200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
20	chr19:53583800-53589200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr19:53584000-53599000	Strong transcription	Muscle Satellite Cultured Cells	--
22	chr19:53584200-53588000	Weak transcription	HMEC	breast
23	chr19:53584200-53588400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr19:53584200-53595000	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr19:53584200-53595200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr19:53584400-53595200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr19:53584400-53596400	Strong transcription	Fetal Brain Female	brain
28	chr19:53584400-53598000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr19:53584600-53588200	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr19:53584600-53589600	Strong transcription	Fetal Muscle Trunk	muscle
31	chr19:53584600-53594600	Strong transcription	Stomach Smooth Muscle	stomach
32	chr19:53584600-53595000	Strong transcription	Brain Cingulate Gyrus	brain
33	chr19:53584600-53599400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr19:53584600-53599800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr19:53584800-53595400	Strong transcription	Brain Germinal Matrix	brain
36	chr19:53585000-53588200	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
37	chr19:53585000-53595200	Strong transcription	Skeletal Muscle Female	skeletal muscle
38	chr19:53585000-53597000	Strong transcription	Primary B cells from peripheral blood	blood
39	chr19:53585200-53589600	Strong transcription	Left Ventricle	heart
40	chr19:53585200-53590000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr19:53585200-53590000	Strong transcription	Brain Hippocampus Middle	brain
42	chr19:53585200-53590600	ZNF genes & repeats	Lung	lung
43	chr19:53585200-53596200	Strong transcription	Thymus	Thymus
44	chr19:53585200-53596400	Strong transcription	Dnd41	blood
45	chr19:53585200-53597800	Strong transcription	Placenta	Placenta
46	chr19:53585200-53599400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr19:53585200-53599600	Strong transcription	Rectal Mucosa Donor 29	rectum
48	chr19:53585400-53589600	Strong transcription	A549	lung
49	chr19:53585400-53590000	Strong transcription	Osteobl	bone
50	chr19:53585400-53590600	Strong transcription	Placenta Amnion	Placenta Amnion

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