Variant report

Variant	rs2384687
Chromosome Location	chr19:55831188-55831189
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10401201	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10411773	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10412726	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10420693	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10425848	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11084393	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1109368	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11668309	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11668344	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1172821	0.95[ASN][1000 genomes]
rs1172822	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11882930	1.00[ASN][1000 genomes]
rs1551562	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs2384686	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2384688	1.00[ASN][1000 genomes]
rs2384689	1.00[ASN][1000 genomes]
rs2384690	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2384691	1.00[ASN][1000 genomes]
rs28875253	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34962991	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35515212	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4806659	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4806660	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4806661	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs734518	0.84[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7508682	0.97[ASN][1000 genomes]
rs8107664	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs897796	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs897797	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs897798	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]

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	esv1816335	chr19:55683977-55901099	Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	nsv1065760	chr19:55721521-55929740	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	212 gene(s)	inside rSNPs	diseases
3	nsv912455	chr19:55725410-55879872	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
4	nsv912456	chr19:55725410-55925500	Weak transcription Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	212 gene(s)	inside rSNPs	diseases
5	nsv912457	chr19:55725410-56019597	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	228 gene(s)	inside rSNPs	diseases
6	nsv912459	chr19:55791380-55845386	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
7	nsv432086	chr19:55807586-56050844	Weak transcription Bivalent Enhancer Genic enhancers Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS 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	220 gene(s)	inside rSNPs	diseases
8	nsv912460	chr19:55814881-55897327	Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	99 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2384687	ZNF587	cis	cerebellum	SCAN
rs2384687	ZNF416	cis	parietal	SCAN
rs2384687	ZNF264	cis	cerebellum	SCAN
rs2384687	RPS5	cis	cerebellum	SCAN

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:55813600-55850000	Weak transcription	Right Atrium	heart
2	chr19:55814400-55831400	Weak transcription	Primary hematopoietic stem cells	blood
3	chr19:55818200-55832400	Weak transcription	Colonic Mucosa	Colon
4	chr19:55818600-55831200	Weak transcription	Right Ventricle	heart
5	chr19:55820800-55839000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr19:55821000-55831200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr19:55821800-55831200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr19:55822000-55831400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr19:55822200-55831400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr19:55822200-55831400	Weak transcription	Brain Anterior Caudate	brain
11	chr19:55822200-55831400	Weak transcription	Brain Cingulate Gyrus	brain
12	chr19:55822200-55831400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr19:55822200-55831400	Weak transcription	Brain Substantia Nigra	brain
14	chr19:55823200-55831400	Weak transcription	Brain Angular Gyrus	brain
15	chr19:55824000-55832200	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr19:55824000-55832400	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr19:55824600-55831400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr19:55824800-55831200	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr19:55824800-55831400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr19:55824800-55831400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr19:55824800-55832200	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr19:55825000-55831200	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr19:55825200-55831400	Weak transcription	Adipose Nuclei	Adipose
24	chr19:55825200-55831400	Weak transcription	Brain Hippocampus Middle	brain
25	chr19:55825600-55832400	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr19:55826400-55831400	Weak transcription	K562	blood
27	chr19:55827800-55831400	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr19:55827800-55832600	Weak transcription	Spleen	Spleen
29	chr19:55827800-55833000	Weak transcription	A549	lung
30	chr19:55828000-55832000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr19:55828000-55832400	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr19:55828400-55831200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr19:55828400-55831200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr19:55828400-55831200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr19:55828400-55833600	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr19:55828600-55831200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr19:55828600-55834400	Weak transcription	Lung	lung
38	chr19:55828800-55831400	Weak transcription	Duodenum Mucosa	Duodenum
39	chr19:55829600-55831400	Weak transcription	Left Ventricle	heart
40	chr19:55831000-55831200	Flanking Active TSS	H1 Cell Line	embryonic stem cell
41	chr19:55831000-55831200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
42	chr19:55831000-55831200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
43	chr19:55831000-55831200	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
44	chr19:55831000-55831200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
45	chr19:55831000-55831200	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr19:55831000-55831200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr19:55831000-55831200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
48	chr19:55831000-55831200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
49	chr19:55831000-55831200	Active TSS	Ovary	ovary
50	chr19:55831000-55831400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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