Variant report

Variant	rs1474460
Chromosome Location	chr19:20220418-20220419
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1097511	0.97[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1230351	0.97[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1230352	0.97[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1474461	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1621688	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1654265	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1654266	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1654267	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1654268	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1654270	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1654271	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1654300	0.91[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1725924	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1725925	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1725926	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1725927	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1725928	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1725929	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35182431	0.92[AMR][1000 genomes]
rs836912	0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519535	chr19:19871250-20595412	Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases
2	esv3319016	chr19:19917475-20819154	Weak transcription ZNF genes & repeats Bivalent Enhancer Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases
3	esv3319017	chr19:19917475-20819154	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer 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	56 gene(s)	inside rSNPs	diseases
4	nsv1061846	chr19:19946927-20595412	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
5	esv3390957	chr19:19965887-20819154	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	53 gene(s)	inside rSNPs	diseases
6	nsv869122	chr19:19969851-20595412	ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription 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	47 gene(s)	inside rSNPs	diseases
7	nsv1059158	chr19:19973489-20576161	Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	43 gene(s)	inside rSNPs	diseases
8	nsv870354	chr19:20043821-20576175	ZNF genes & repeats Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
9	nsv1066004	chr19:20053658-20592867	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
10	nsv543932	chr19:20053658-20592867	Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
11	nsv1066564	chr19:20056348-20595412	Weak transcription Active TSS ZNF genes & repeats Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
12	nsv1066375	chr19:20061084-20574512	Strong transcription ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	31 gene(s)	inside rSNPs	diseases
13	nsv543934	chr19:20061084-20574512	Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	31 gene(s)	inside rSNPs	diseases
14	nsv1057309	chr19:20072886-20595412	Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
15	nsv578801	chr19:20084681-20595412	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	33 gene(s)	inside rSNPs	diseases
16	nsv1055694	chr19:20088866-20595412	Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	33 gene(s)	inside rSNPs	diseases
17	nsv578802	chr19:20091702-20595412	ZNF genes & repeats Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	33 gene(s)	inside rSNPs	diseases
18	nsv1064400	chr19:20101052-20595412	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers 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	33 gene(s)	inside rSNPs	diseases
19	nsv911325	chr19:20151257-21071548	ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	49 gene(s)	inside rSNPs	diseases
20	nsv1066014	chr19:20165112-20595412	Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1474460	ZNF682	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:20207600-20240400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:20207600-20240600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr19:20207600-20241200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr19:20208000-20222400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr19:20209400-20221800	Weak transcription	Rectal Smooth Muscle	rectum
6	chr19:20209400-20239000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr19:20211400-20238800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
8	chr19:20213400-20222000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr19:20214000-20227200	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr19:20214200-20220600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr19:20214600-20225000	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr19:20215200-20223800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr19:20215200-20240400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
14	chr19:20215400-20223200	Strong transcription	H1 Cell Line	embryonic stem cell
15	chr19:20215600-20221000	Weak transcription	Stomach Smooth Muscle	stomach
16	chr19:20215600-20225000	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr19:20216000-20222200	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
18	chr19:20216200-20221600	Strong transcription	Cortex derived primary cultured neurospheres	brain
19	chr19:20216600-20224000	Weak transcription	Fetal Brain Male	brain
20	chr19:20216600-20224000	Weak transcription	Fetal Kidney	kidney
21	chr19:20217000-20225200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
22	chr19:20217000-20238400	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
23	chr19:20217200-20225200	ZNF genes & repeats	Fetal Intestine Small	intestine
24	chr19:20217200-20234400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
25	chr19:20217600-20223200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr19:20217800-20237200	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
27	chr19:20218200-20221200	Weak transcription	Pancreas	Pancrea
28	chr19:20218200-20222000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr19:20218200-20226600	Weak transcription	NHDF-Ad	bronchial
30	chr19:20218600-20221000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr19:20218800-20220800	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr19:20218800-20221000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr19:20219000-20221600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr19:20219200-20221400	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr19:20219400-20221200	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr19:20219600-20222000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr19:20219600-20234200	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
38	chr19:20219600-20234800	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
39	chr19:20219800-20221200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr19:20219800-20221200	Weak transcription	Aorta	Aorta
41	chr19:20219800-20223200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr19:20219800-20223200	Weak transcription	Gastric	stomach
43	chr19:20220000-20220800	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr19:20220000-20221000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr19:20220000-20222000	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr19:20220000-20222000	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr19:20220200-20220600	ZNF genes & repeats	Ovary	ovary
48	chr19:20220200-20222600	Strong transcription	Fetal Lung	lung

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