Variant report

Variant	rs1725926
Chromosome Location	chr19:20218177-20218178
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1097511	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1230351	0.84[ASN][1000 genomes]
rs1230352	0.84[ASN][1000 genomes]
rs12459266	0.81[EUR][1000 genomes]
rs1474460	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1474461	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1621688	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1654265	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1654266	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1654267	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1654268	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1654270	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1654271	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1654300	0.84[ASN][1000 genomes]
rs1725924	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1725925	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1725927	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1725928	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1725929	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs836909	0.89[EUR][1000 genomes]
rs865075	0.89[EUR][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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs1725926	ZNF682	Cis_1M	lymphoblastoid	RTeQTL
rs1725926	ZNF682	cis	Muscle Skeletal	GTEx
rs1725926	ZNF486	cis	cerebellum	SCAN
rs1725926	ZNF682	cis	cerebellum	SCAN
rs1725926	ZNF93	cis	cerebellum	SCAN
rs1725926	F2RL3	cis	parietal	SCAN
rs1725926	ZNF682	cis	parietal	SCAN
rs1725926	ZNF506	cis	parietal	SCAN
rs1725926	ATP13A1	cis	parietal	SCAN
rs1725926	GTPBP3	cis	parietal	SCAN

Chromatin state (count:81 , 50 per page) page: 1 2

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	chr19:20207800-20218400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr19:20208000-20222400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr19:20209400-20221800	Weak transcription	Rectal Smooth Muscle	rectum
7	chr19:20209400-20239000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr19:20211400-20238800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
9	chr19:20213400-20222000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr19:20214000-20227200	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr19:20214200-20220600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr19:20214600-20219200	Weak transcription	Right Ventricle	heart
13	chr19:20214600-20225000	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr19:20215000-20218600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr19:20215200-20223800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr19:20215200-20240400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
17	chr19:20215400-20219000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr19:20215400-20223200	Strong transcription	H1 Cell Line	embryonic stem cell
19	chr19:20215600-20221000	Weak transcription	Stomach Smooth Muscle	stomach
20	chr19:20215600-20225000	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr19:20216000-20218600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
22	chr19:20216000-20222200	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
23	chr19:20216200-20219000	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr19:20216200-20221600	Strong transcription	Cortex derived primary cultured neurospheres	brain
25	chr19:20216600-20219600	Strong transcription	HUES48 Cell Line	embryonic stem cell
26	chr19:20216600-20224000	Weak transcription	Fetal Brain Male	brain
27	chr19:20216600-20224000	Weak transcription	Fetal Kidney	kidney
28	chr19:20217000-20225200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
29	chr19:20217000-20238400	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
30	chr19:20217200-20218200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr19:20217200-20218200	ZNF genes & repeats	Fetal Stomach	stomach
32	chr19:20217200-20218400	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr19:20217200-20218400	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr19:20217200-20218400	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
35	chr19:20217200-20219400	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
36	chr19:20217200-20225200	ZNF genes & repeats	Fetal Intestine Small	intestine
37	chr19:20217200-20234400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
38	chr19:20217400-20218400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
39	chr19:20217400-20218400	ZNF genes & repeats	Left Ventricle	heart
40	chr19:20217400-20220200	ZNF genes & repeats	Fetal Lung	lung
41	chr19:20217600-20218200	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr19:20217600-20218200	ZNF genes & repeats	Esophagus	oesophagus
43	chr19:20217600-20218200	Strong transcription	Pancreas	Pancrea
44	chr19:20217600-20218400	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr19:20217600-20218400	ZNF genes & repeats	Primary B cells from peripheral blood	blood
46	chr19:20217600-20218400	ZNF genes & repeats	Aorta	Aorta
47	chr19:20217600-20218400	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
48	chr19:20217600-20218400	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
49	chr19:20217600-20218600	ZNF genes & repeats	Primary B cells from cord blood	blood
50	chr19:20217600-20218600	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood

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