Variant report

Variant	rs1725925
Chromosome Location	chr19:20217944-20217945
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1097511	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1230351	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1230352	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1474460	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1474461	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1621688	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1654265	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1654266	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1654267	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1654268	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1654270	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1654271	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1654300	0.91[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1725924	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1725926	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1725927	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1725928	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1725929	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35182431	0.92[AMR][1000 genomes]
rs836912	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1725925	ZNF682	Cis_1M	lymphoblastoid	RTeQTL
rs1725925	ZNF506	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:84 , 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	chr19:20210000-20218000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr19:20211400-20238800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
10	chr19:20213400-20222000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr19:20214000-20227200	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr19:20214200-20218000	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr19:20214200-20220600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr19:20214400-20218000	Weak transcription	Fetal Thymus	thymus
15	chr19:20214600-20219200	Weak transcription	Right Ventricle	heart
16	chr19:20214600-20225000	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr19:20215000-20218600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr19:20215200-20223800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr19:20215200-20240400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
20	chr19:20215400-20219000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr19:20215400-20223200	Strong transcription	H1 Cell Line	embryonic stem cell
22	chr19:20215600-20221000	Weak transcription	Stomach Smooth Muscle	stomach
23	chr19:20215600-20225000	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr19:20216000-20218600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
25	chr19:20216000-20222200	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
26	chr19:20216200-20219000	Weak transcription	Primary T cells fromperipheralblood	blood
27	chr19:20216200-20221600	Strong transcription	Cortex derived primary cultured neurospheres	brain
28	chr19:20216600-20219600	Strong transcription	HUES48 Cell Line	embryonic stem cell
29	chr19:20216600-20224000	Weak transcription	Fetal Brain Male	brain
30	chr19:20216600-20224000	Weak transcription	Fetal Kidney	kidney
31	chr19:20217000-20218000	Weak transcription	NHDF-Ad	bronchial
32	chr19:20217000-20225200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
33	chr19:20217000-20238400	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
34	chr19:20217200-20218200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr19:20217200-20218200	ZNF genes & repeats	Fetal Stomach	stomach
36	chr19:20217200-20218400	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr19:20217200-20218400	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr19:20217200-20218400	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
39	chr19:20217200-20219400	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
40	chr19:20217200-20225200	ZNF genes & repeats	Fetal Intestine Small	intestine
41	chr19:20217200-20234400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
42	chr19:20217400-20218400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
43	chr19:20217400-20218400	ZNF genes & repeats	Left Ventricle	heart
44	chr19:20217400-20220200	ZNF genes & repeats	Fetal Lung	lung
45	chr19:20217600-20218000	ZNF genes & repeats	Brain Hippocampus Middle	brain
46	chr19:20217600-20218000	ZNF genes & repeats	Osteobl	bone
47	chr19:20217600-20218200	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr19:20217600-20218200	ZNF genes & repeats	Esophagus	oesophagus
49	chr19:20217600-20218200	Strong transcription	Pancreas	Pancrea
50	chr19:20217600-20218400	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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