Variant report

Variant	rs4507016
Chromosome Location	chr19:52089724-52089725
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	chr19:52055102..52056750-chr19:52089183..52091474,2	K562	blood:

Extended variants
information (count: 18 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11665668	1.00[CHB][hapmap]
rs12977262	1.00[CHB][hapmap]
rs1543923	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3826666	1.00[CHB][hapmap]
rs4802815	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4802818	0.82[CEU][hapmap];1.00[CHB][hapmap];0.82[MEX][hapmap]
rs6509553	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6509554	0.91[CEU][hapmap]
rs6509555	0.87[CEU][hapmap]
rs8108074	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1066308	chr19:51680133-52103974	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv544049	chr19:51680133-52103974	Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
3	nsv544051	chr19:51944903-52147459	Bivalent Enhancer Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	esv2758504	chr19:51991896-52266700	Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	542 gene(s)	inside rSNPs	diseases
5	esv2758767	chr19:51991896-52604625	Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	578 gene(s)	inside rSNPs	diseases
6	nsv469584	chr19:52001381-52151821	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
7	nsv482654	chr19:52001381-52151821	Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
8	nsv579966	chr19:52075622-52131119	Enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4507016	NLRP2	cis	cerebellum	SCAN
rs4507016	TMEM150B	cis	cerebellum	SCAN
rs4507016	ZNF321	cis	cerebellum	SCAN
rs4507016	CACNG7	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52075400-52090200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr19:52075800-52090000	Weak transcription	Stomach Mucosa	stomach
3	chr19:52075800-52096800	Weak transcription	HepG2	liver
4	chr19:52077000-52097000	Weak transcription	Hela-S3	cervix
5	chr19:52081400-52091000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr19:52081600-52092000	ZNF genes & repeats	Liver	Liver
7	chr19:52082200-52090000	Strong transcription	Placenta	Placenta
8	chr19:52083600-52090600	Strong transcription	Cortex derived primary cultured neurospheres	brain
9	chr19:52083800-52090000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr19:52083800-52091000	Strong transcription	Brain Hippocampus Middle	brain
11	chr19:52084000-52090000	Strong transcription	Skeletal Muscle Male	skeletal muscle
12	chr19:52084000-52091400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr19:52084000-52091400	Strong transcription	Fetal Intestine Large	intestine
14	chr19:52084200-52090200	Strong transcription	Stomach Smooth Muscle	stomach
15	chr19:52084200-52091600	Strong transcription	Fetal Thymus	thymus
16	chr19:52084600-52091200	Strong transcription	Placenta Amnion	Placenta Amnion
17	chr19:52084800-52089800	Strong transcription	Fetal Brain Male	brain
18	chr19:52084800-52091400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr19:52085400-52089800	Weak transcription	Colonic Mucosa	Colon
20	chr19:52086600-52091600	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
21	chr19:52086600-52093200	ZNF genes & repeats	K562	blood
22	chr19:52086800-52091000	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
23	chr19:52086800-52091600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr19:52086800-52091800	ZNF genes & repeats	A549	lung
25	chr19:52086800-52092000	ZNF genes & repeats	Primary T cells from cord blood	blood
26	chr19:52087000-52090000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr19:52087000-52091200	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
28	chr19:52087000-52091800	ZNF genes & repeats	Primary T killer memory cells from peripheral blood	blood
29	chr19:52087000-52091800	ZNF genes & repeats	GM12878-XiMat	blood
30	chr19:52087000-52092000	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
31	chr19:52087200-52090200	Strong transcription	Left Ventricle	heart
32	chr19:52087400-52091800	ZNF genes & repeats	Osteobl	bone
33	chr19:52087400-52092000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr19:52087400-52092600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
35	chr19:52087600-52091800	ZNF genes & repeats	Primary B cells from cord blood	blood
36	chr19:52087600-52091800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr19:52087800-52090800	Strong transcription	Psoas Muscle	Psoas
38	chr19:52087800-52091000	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
39	chr19:52087800-52091400	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
40	chr19:52087800-52091800	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
41	chr19:52088000-52091800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr19:52088000-52092000	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr19:52088200-52092000	ZNF genes & repeats	Primary B cells from peripheral blood	blood
44	chr19:52088400-52091400	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
45	chr19:52088400-52091800	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr19:52088600-52092000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr19:52088600-52092000	ZNF genes & repeats	HUVEC	blood vessel
48	chr19:52088800-52091600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr19:52089000-52090000	Enhancers	Primary monocytes fromperipheralblood	blood
50	chr19:52089000-52090800	ZNF genes & repeats	Primary T helper naive cells from peripheral blood	blood

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