Variant report

Variant	rs17707446
Chromosome Location	chr19:37583042-37583043
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF568-3	chr19:37582243-37583466	ENSG00000267672.1

Extended variants
information (count: 51 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1047333	0.92[CEU][hapmap];0.82[GIH][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes]
rs11540540	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11667146	0.88[CEU][hapmap];0.80[TSI][hapmap]
rs11668615	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11670374	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11671112	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11673192	0.80[EUR][1000 genomes]
rs11673344	0.81[CEU][hapmap]
rs12151313	0.83[EUR][1000 genomes]
rs1533736	0.92[CEU][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.92[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1879497	0.88[CEU][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs320887	1.00[JPT][hapmap]
rs3745768	0.84[CEU][hapmap]
rs3745770	0.84[CEU][hapmap]
rs496872	0.81[CEU][hapmap]
rs513406	0.81[CEU][hapmap]
rs547483	0.81[CEU][hapmap]
rs55856280	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56080874	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56161518	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56210764	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56248021	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56343212	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7248693	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7255595	1.00[JPT][hapmap]
rs7256746	0.81[CEU][hapmap]
rs7256876	0.85[EUR][1000 genomes]
rs7257135	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7259513	0.85[EUR][1000 genomes]
rs7260386	0.88[CEU][hapmap]
rs73039116	1.00[ASN][1000 genomes]
rs73039188	1.00[ASN][1000 genomes]
rs8108727	0.87[CEU][hapmap];0.86[EUR][1000 genomes]
rs826296	0.80[CEU][hapmap]
rs826303	0.81[CEU][hapmap]
rs826304	0.81[CEU][hapmap]
rs862234	1.00[YRI][hapmap]

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	nsv833818	chr19:37427808-37602800	Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
13	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
14	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

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs17707446	CEACAM16	cis	cerebellum	SCAN
rs17707446	ZNF781	cis	Thyroid	GTEx
rs17707446	MED29	cis	cerebellum	SCAN
rs17707446	AC012309.5	cis	Esophagus Muscularis	GTEx
rs17707446	AC012309.5	cis	Heart Left Ventricle	GTEx
rs17707446	AC012309.5	cis	Thyroid	GTEx
rs17707446	HKR1	cis	multi-tissue	Pritchard
rs17707446	ZNF585B	cis	Artery Tibial	GTEx
rs17707446	AC012309.5	cis	Artery Tibial	GTEx
rs17707446	AC012309.5	cis	Esophagus Mucosa	GTEx
rs17707446	ZNF585A	Cis_1M	lymphoblastoid	RTeQTL
rs17707446	ARHGEF1	cis	cerebellum	SCAN
rs17707446	RYR1	cis	cerebellum	SCAN

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37571000-37594800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr19:37572400-37594600	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
3	chr19:37572600-37595400	ZNF genes & repeats	Adipose Nuclei	Adipose
4	chr19:37572800-37594600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
5	chr19:37572800-37594800	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
6	chr19:37572800-37595400	ZNF genes & repeats	Liver	Liver
7	chr19:37575400-37592400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr19:37575400-37595200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr19:37575800-37594800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
10	chr19:37576000-37587800	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
11	chr19:37576200-37588000	ZNF genes & repeats	Fetal Muscle Trunk	muscle
12	chr19:37576200-37591200	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
13	chr19:37576200-37595600	ZNF genes & repeats	Ovary	ovary
14	chr19:37576200-37595800	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
15	chr19:37577400-37592400	Strong transcription	Skeletal Muscle Male	skeletal muscle
16	chr19:37578800-37583200	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 1	blood
17	chr19:37578800-37585600	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
18	chr19:37578800-37585600	ZNF genes & repeats	Primary T cells from cord blood	blood
19	chr19:37578800-37594600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
20	chr19:37578800-37594800	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr19:37579000-37585000	ZNF genes & repeats	Fetal Lung	lung
22	chr19:37579000-37585400	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
23	chr19:37579000-37587800	ZNF genes & repeats	Primary B cells from cord blood	blood
24	chr19:37579000-37594800	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
25	chr19:37579200-37588000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr19:37579200-37593800	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
27	chr19:37579400-37583800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr19:37579400-37594800	ZNF genes & repeats	Duodenum Mucosa	Duodenum
29	chr19:37579600-37595400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr19:37579800-37583200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr19:37579800-37583400	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
32	chr19:37579800-37584000	Strong transcription	Left Ventricle	heart
33	chr19:37579800-37584400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr19:37579800-37584600	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
35	chr19:37579800-37584800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr19:37579800-37584800	ZNF genes & repeats	Fetal Kidney	kidney
37	chr19:37579800-37584800	ZNF genes & repeats	Thymus	Thymus
38	chr19:37579800-37585000	Strong transcription	Brain Anterior Caudate	brain
39	chr19:37579800-37585000	Strong transcription	Placenta	Placenta
40	chr19:37579800-37585200	ZNF genes & repeats	GM12878-XiMat	blood
41	chr19:37579800-37585400	Strong transcription	Brain Inferior Temporal Lobe	brain
42	chr19:37579800-37585600	Strong transcription	Brain Cingulate Gyrus	brain
43	chr19:37579800-37586000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr19:37579800-37587400	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
45	chr19:37579800-37587400	ZNF genes & repeats	Brain Germinal Matrix	brain
46	chr19:37579800-37590200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
47	chr19:37579800-37591200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr19:37579800-37594800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
49	chr19:37579800-37595000	ZNF genes & repeats	Fetal Brain Female	brain
50	chr19:37580000-37583200	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin

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