Variant report

Variant	rs1610560
Chromosome Location	chr19:37642385-37642386
allele	A/C
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: 51 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1047333	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11084871	0.93[ASN][1000 genomes]
rs11667146	0.86[ASN][1000 genomes]
rs11670216	0.89[ASN][1000 genomes]
rs11673192	0.93[ASN][1000 genomes]
rs1234251	0.80[EUR][1000 genomes]
rs16971886	0.84[ASN][1000 genomes]
rs1879497	0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1962889	0.84[EUR][1000 genomes]
rs2011475	0.93[ASN][1000 genomes]
rs2562587	0.89[ASN][1000 genomes]
rs3745768	0.84[ASN][1000 genomes]
rs3745770	0.84[ASN][1000 genomes]
rs55792845	0.89[ASN][1000 genomes]
rs55921822	0.89[ASN][1000 genomes]
rs56208574	0.89[ASN][1000 genomes]
rs57916401	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs703530	0.89[ASN][1000 genomes]
rs703535	0.89[ASN][1000 genomes]
rs703537	0.89[ASN][1000 genomes]
rs7247589	0.89[ASN][1000 genomes]
rs7252230	0.89[ASN][1000 genomes]
rs7254616	0.86[ASN][1000 genomes]
rs7256213	0.89[ASN][1000 genomes]
rs7256746	0.84[EUR][1000 genomes]
rs7256876	0.93[ASN][1000 genomes]
rs7259513	0.93[ASN][1000 genomes]
rs7260386	0.86[EUR][1000 genomes]
rs73622783	0.83[EUR][1000 genomes]
rs8104919	0.89[ASN][1000 genomes]
rs8106386	0.89[ASN][1000 genomes]
rs8107192	0.89[ASN][1000 genomes]
rs8108727	0.93[ASN][1000 genomes]
rs8110696	0.89[ASN][1000 genomes]
rs826322	0.89[ASN][1000 genomes]
rs826323	0.89[ASN][1000 genomes]
rs9676450	0.84[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1610560	ZNF585A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37613800-37662200	ZNF genes & repeats	Liver	Liver
2	chr19:37634400-37657800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr19:37634800-37642600	ZNF genes & repeats	Brain Germinal Matrix	brain
4	chr19:37635000-37656200	ZNF genes & repeats	Fetal Brain Female	brain
5	chr19:37635200-37661400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
6	chr19:37635200-37661600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr19:37635800-37642800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr19:37637400-37656800	ZNF genes & repeats	Brain Anterior Caudate	brain
9	chr19:37637600-37642400	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr19:37639400-37643800	Weak transcription	Stomach Mucosa	stomach
11	chr19:37639400-37663200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr19:37640000-37643400	Weak transcription	Fetal Heart	heart
13	chr19:37640200-37642400	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
14	chr19:37640400-37642400	ZNF genes & repeats	Brain Cingulate Gyrus	brain
15	chr19:37640400-37642600	ZNF genes & repeats	Placenta	Placenta
16	chr19:37640400-37648000	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr19:37640400-37659000	ZNF genes & repeats	Primary B cells from peripheral blood	blood
18	chr19:37641600-37643800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr19:37641800-37642400	Strong transcription	Skeletal Muscle Female	skeletal muscle
20	chr19:37641800-37643200	Weak transcription	Fetal Kidney	kidney
21	chr19:37641800-37643200	Weak transcription	Rectal Smooth Muscle	rectum
22	chr19:37641800-37643400	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr19:37641800-37643400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr19:37641800-37643400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr19:37641800-37643400	Weak transcription	Fetal Intestine Large	intestine
26	chr19:37641800-37643400	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr19:37642000-37643200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr19:37642000-37643200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr19:37642000-37643200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr19:37642000-37643200	Weak transcription	Fetal Brain Male	brain
31	chr19:37642000-37643200	Weak transcription	Left Ventricle	heart
32	chr19:37642000-37643200	Weak transcription	Psoas Muscle	Psoas
33	chr19:37642000-37643200	Weak transcription	Right Ventricle	heart
34	chr19:37642000-37643400	Weak transcription	Brain Angular Gyrus	brain
35	chr19:37642000-37643400	Weak transcription	Fetal Muscle Trunk	muscle
36	chr19:37642000-37643400	Weak transcription	Gastric	stomach
37	chr19:37642000-37643400	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr19:37642000-37643400	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr19:37642000-37643800	Weak transcription	Primary T cells from cord blood	blood
40	chr19:37642000-37643800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr19:37642000-37646000	Weak transcription	Pancreas	Pancrea
42	chr19:37642200-37643000	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr19:37642200-37643200	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr19:37642200-37643200	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr19:37642200-37643200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr19:37642200-37643200	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr19:37642200-37643200	Weak transcription	Ovary	ovary
48	chr19:37642200-37643400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr19:37642200-37643400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr19:37642200-37643400	Weak transcription	Primary T helper cells PMA-I stimulated	--

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