Variant report

Variant	rs1047333
Chromosome Location	chr19:37642165-37642166
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF420-1	chr19:37642073-37643211	NONHSAT066073

Extended variants
information (count: 69 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs11084871	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11540540	0.87[EUR][1000 genomes]
rs11667146	0.96[CEU][hapmap];0.84[GIH][hapmap];0.92[TSI][hapmap];0.84[EUR][1000 genomes]
rs11670216	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11670374	0.85[EUR][1000 genomes]
rs11671112	0.87[EUR][1000 genomes]
rs11673192	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11673344	0.88[CEU][hapmap];0.85[GIH][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes]
rs12151313	0.89[EUR][1000 genomes]
rs1234251	0.88[EUR][1000 genomes]
rs1533736	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs1610560	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1657510	0.86[CHB][hapmap]
rs16972020	0.86[CHB][hapmap]
rs16972024	0.86[CHB][hapmap]
rs16972028	0.86[CHB][hapmap]
rs16972030	0.86[CHB][hapmap]
rs17707446	0.92[CEU][hapmap];0.82[GIH][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes]
rs1879497	0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1962889	0.86[EUR][1000 genomes]
rs2011475	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2562587	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3745768	0.92[CEU][hapmap]
rs3745770	0.92[CEU][hapmap]
rs45626541	0.88[EUR][1000 genomes]
rs55792845	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55856280	0.90[EUR][1000 genomes]
rs55921822	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56080874	0.85[EUR][1000 genomes]
rs56208574	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56210764	0.85[EUR][1000 genomes]
rs56330606	0.91[EUR][1000 genomes]
rs56343212	0.87[EUR][1000 genomes]
rs703530	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs703535	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs703537	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7247589	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7252230	0.81[ASN][1000 genomes]
rs7254616	0.82[EUR][1000 genomes]
rs7256213	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7256746	0.88[CEU][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs7256876	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7257135	0.92[CEU][hapmap];0.82[GIH][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs7259513	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7260386	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs73622783	0.86[EUR][1000 genomes]
rs8104919	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8106386	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8107192	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8108727	0.96[CEU][hapmap];0.86[CHB][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8110696	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs826303	0.88[CEU][hapmap]
rs826304	0.88[CEU][hapmap];0.90[TSI][hapmap]
rs826322	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs826323	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064851	chr19:36910259-37689721	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv1065698	chr19:36916796-37690124	Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv543999	chr19:36916796-37690124	Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv529817	chr19:36930549-37654062	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
5	nsv918028	chr19:37020645-38014526	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
6	esv3507199	chr19:37284708-37805639	Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
7	esv3507200	chr19:37284708-37805639	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
8	esv3497360	chr19:37290273-37745365	ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
9	esv3497361	chr19:37290273-37745365	Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers 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
10	nsv458568	chr19:37325826-37747108	Strong transcription ZNF genes & repeats Genic enhancers Active TSS Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
11	nsv579461	chr19:37325826-37747108	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
12	nsv911652	chr19:37437106-37774299	Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers 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	17 gene(s)	inside rSNPs	diseases
13	nsv911654	chr19:37487632-37758082	Strong transcription Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
14	nsv2477	chr19:37617348-37662207	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs1047333	AC012309.5	cis	Esophagus Mucosa	GTEx
rs1047333	AC012309.5	cis	Heart Left Ventricle	GTEx
rs1047333	CEACAM16	cis	cerebellum	SCAN
rs1047333	ZNF585A	Cis_1M	lymphoblastoid	RTeQTL
rs1047333	ZNF585B	cis	Artery Tibial	GTEx
rs1047333	AC012309.5	cis	Thyroid	GTEx
rs1047333	AC012309.5	cis	Esophagus Muscularis	GTEx
rs1047333	ARHGEF1	cis	cerebellum	SCAN
rs1047333	AC012309.5	cis	Artery Tibial	GTEx

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37613400-37642200	ZNF genes & repeats	Adipose Nuclei	Adipose
2	chr19:37613400-37642200	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
3	chr19:37613800-37662200	ZNF genes & repeats	Liver	Liver
4	chr19:37634400-37657800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr19:37634800-37642600	ZNF genes & repeats	Brain Germinal Matrix	brain
6	chr19:37635000-37642200	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr19:37635000-37656200	ZNF genes & repeats	Fetal Brain Female	brain
8	chr19:37635200-37642200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
9	chr19:37635200-37642200	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
10	chr19:37635200-37642200	ZNF genes & repeats	Fetal Lung	lung
11	chr19:37635200-37642200	ZNF genes & repeats	Ovary	ovary
12	chr19:37635200-37661400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
13	chr19:37635200-37661600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr19:37635400-37642200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr19:37635600-37642200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr19:37635600-37642200	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
17	chr19:37635800-37642200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
18	chr19:37635800-37642800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr19:37637400-37642200	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
20	chr19:37637400-37642200	ZNF genes & repeats	Brain Hippocampus Middle	brain
21	chr19:37637400-37642200	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
22	chr19:37637400-37642200	ZNF genes & repeats	Dnd41	blood
23	chr19:37637400-37656800	ZNF genes & repeats	Brain Anterior Caudate	brain
24	chr19:37637600-37642200	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
25	chr19:37637600-37642400	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr19:37638800-37642200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr19:37639000-37642200	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
28	chr19:37639000-37642200	ZNF genes & repeats	Brain Substantia Nigra	brain
29	chr19:37639400-37642200	ZNF genes & repeats	Brain Dorsolateral Prefrontal Cortex	brain
30	chr19:37639400-37643800	Weak transcription	Stomach Mucosa	stomach
31	chr19:37639400-37663200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr19:37639600-37642200	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
33	chr19:37639800-37642200	ZNF genes & repeats	Stomach Smooth Muscle	stomach
34	chr19:37640000-37642200	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
35	chr19:37640000-37643400	Weak transcription	Fetal Heart	heart
36	chr19:37640200-37642400	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
37	chr19:37640400-37642400	ZNF genes & repeats	Brain Cingulate Gyrus	brain
38	chr19:37640400-37642600	ZNF genes & repeats	Placenta	Placenta
39	chr19:37640400-37648000	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr19:37640400-37659000	ZNF genes & repeats	Primary B cells from peripheral blood	blood
41	chr19:37640600-37642200	ZNF genes & repeats	HSMMtube	muscle
42	chr19:37640800-37642200	ZNF genes & repeats	Primary B cells from cord blood	blood
43	chr19:37641200-37642200	ZNF genes & repeats	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr19:37641600-37643800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr19:37641800-37642400	Strong transcription	Skeletal Muscle Female	skeletal muscle
46	chr19:37641800-37643200	Weak transcription	Fetal Kidney	kidney
47	chr19:37641800-37643200	Weak transcription	Rectal Smooth Muscle	rectum
48	chr19:37641800-37643400	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr19:37641800-37643400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr19:37641800-37643400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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