Variant report

Variant	rs365745
Chromosome Location	chr19:44471209-44471210
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10164273	0.85[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10164282	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11666551	0.89[ASN][1000 genomes]
rs11668687	0.85[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11669568	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs11669702	0.89[ASN][1000 genomes]
rs11670342	0.89[ASN][1000 genomes]
rs11670772	0.83[EUR][1000 genomes]
rs11671384	0.89[ASN][1000 genomes]
rs11672879	0.85[EUR][1000 genomes]
rs11673170	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12185486	0.89[ASN][1000 genomes]
rs2284242	0.82[ASN][1000 genomes]
rs2284243	0.86[JPT][hapmap]
rs36044624	0.84[EUR][1000 genomes]
rs366111	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs367358	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs369958	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs380242	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs392160	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs415913	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs425200	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs436788	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs437058	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs437067	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs439676	0.86[LWK][hapmap];0.81[MKK][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes]
rs441794	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs442679	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs445265	0.81[EUR][1000 genomes]
rs452238	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs454218	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs458647	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs460071	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs462417	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55750317	0.84[EUR][1000 genomes]
rs58591332	0.88[EUR][1000 genomes]
rs612663	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61734609	0.89[ASN][1000 genomes]
rs73035922	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73038560	0.82[ASN][1000 genomes]
rs73038602	0.80[ASN][1000 genomes]
rs73050193	0.89[ASN][1000 genomes]
rs73050195	0.89[ASN][1000 genomes]
rs73051806	0.86[ASN][1000 genomes]
rs73051810	0.89[ASN][1000 genomes]
rs73051815	0.89[ASN][1000 genomes]
rs73051825	0.89[ASN][1000 genomes]
rs73051828	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469650	chr19:44405994-44555426	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv579854	chr19:44411543-44490024	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv912109	chr19:44459074-44493142	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs365745	LYPD5	cis	brain	seeQTL
rs365745	CCDC114	cis	parietal	SCAN
rs365745	NR1H2	cis	cerebellum	SCAN
rs365745	ZNF616	cis	cerebellum	SCAN

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44456200-44476600	ZNF genes & repeats	Brain Germinal Matrix	brain
2	chr19:44456400-44479600	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
3	chr19:44456400-44487800	ZNF genes & repeats	Liver	Liver
4	chr19:44456600-44475200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr19:44461800-44475200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
6	chr19:44462000-44475000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr19:44462000-44485200	ZNF genes & repeats	Adipose Nuclei	Adipose
8	chr19:44462200-44474800	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
9	chr19:44462200-44475600	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr19:44462200-44475800	ZNF genes & repeats	Fetal Lung	lung
11	chr19:44462200-44476600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
12	chr19:44462400-44475400	ZNF genes & repeats	Duodenum Mucosa	Duodenum
13	chr19:44462800-44475400	ZNF genes & repeats	Brain Anterior Caudate	brain
14	chr19:44463000-44478800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr19:44463200-44475600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
16	chr19:44463200-44475600	ZNF genes & repeats	Brain Hippocampus Middle	brain
17	chr19:44463400-44476400	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr19:44464000-44475000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr19:44464400-44475800	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
20	chr19:44465600-44475400	ZNF genes & repeats	Fetal Brain Male	brain
21	chr19:44465800-44475400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr19:44466200-44473200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr19:44466200-44475000	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr19:44466200-44475200	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr19:44466200-44475600	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
26	chr19:44466400-44474800	ZNF genes & repeats	Brain Dorsolateral Prefrontal Cortex	brain
27	chr19:44466400-44474800	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
28	chr19:44466400-44474800	ZNF genes & repeats	Ovary	ovary
29	chr19:44466400-44475000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr19:44466400-44475600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr19:44466400-44476200	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
32	chr19:44466400-44480000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr19:44466600-44472800	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
34	chr19:44466600-44474600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
35	chr19:44466600-44474600	ZNF genes & repeats	Dnd41	blood
36	chr19:44466600-44474800	ZNF genes & repeats	Brain Cingulate Gyrus	brain
37	chr19:44466600-44474800	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
38	chr19:44466600-44475000	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr19:44466600-44475000	ZNF genes & repeats	Brain Substantia Nigra	brain
40	chr19:44466600-44475000	ZNF genes & repeats	Rectal Smooth Muscle	rectum
41	chr19:44466600-44475000	ZNF genes & repeats	Stomach Smooth Muscle	stomach
42	chr19:44466600-44475400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr19:44466600-44475400	ZNF genes & repeats	Fetal Muscle Trunk	muscle
44	chr19:44466800-44471600	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
45	chr19:44466800-44473200	ZNF genes & repeats	Primary B cells from cord blood	blood
46	chr19:44466800-44475000	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
47	chr19:44466800-44475000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
48	chr19:44466800-44475000	ZNF genes & repeats	Fetal Kidney	kidney
49	chr19:44466800-44475200	ZNF genes & repeats	Brain Angular Gyrus	brain
50	chr19:44466800-44475400	ZNF genes & repeats	H1 Cell Line	embryonic stem cell

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