Variant report

Variant	rs1678822
Chromosome Location	chr19:21478858-21478859
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 90 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs1012040	1.00[JPT][hapmap]
rs12975981	0.86[CEU][hapmap];1.00[JPT][hapmap]
rs12981869	0.86[CEU][hapmap];1.00[JPT][hapmap]
rs1500401	1.00[JPT][hapmap]
rs17618715	0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs17618778	0.87[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1762580	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17680671	0.85[CHB][hapmap]
rs1813234	1.00[CEU][hapmap]
rs2133820	1.00[JPT][hapmap]
rs2246914	1.00[JPT][hapmap]
rs2358984	1.00[CEU][hapmap]
rs2562448	1.00[JPT][hapmap]
rs2562457	1.00[JPT][hapmap]
rs2562458	1.00[JPT][hapmap]
rs2650779	1.00[JPT][hapmap]
rs2650780	1.00[JPT][hapmap]
rs2650781	1.00[JPT][hapmap]
rs2650783	1.00[JPT][hapmap]
rs2650791	1.00[JPT][hapmap]
rs2650794	1.00[JPT][hapmap]
rs2650845	0.86[CEU][hapmap]
rs279813	0.81[EUR][1000 genomes]
rs2914636	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2914637	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2928210	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34875588	0.82[ASN][1000 genomes]
rs35860067	0.82[ASN][1000 genomes]
rs4341872	0.87[CEU][hapmap]
rs483383	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs488125	1.00[CEU][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs501647	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs504280	0.95[CEU][hapmap];0.86[CHB][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs508888	0.83[ASN][1000 genomes]
rs509540	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs514390	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs531283	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs549882	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs552039	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs565406	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs566230	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57055133	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58121117	0.82[ASN][1000 genomes]
rs59617671	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs597166	0.83[ASN][1000 genomes]
rs600428	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs608002	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs617186	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs617189	0.83[ASN][1000 genomes]
rs619867	0.81[ASN][1000 genomes]
rs620804	0.83[ASN][1000 genomes]
rs62107470	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62107538	0.82[ASN][1000 genomes]
rs62109224	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62110379	0.82[ASN][1000 genomes]
rs629548	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs635730	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs653494	0.83[ASN][1000 genomes]
rs656523	0.83[ASN][1000 genomes]
rs657879	0.83[ASN][1000 genomes]
rs661393	0.83[ASN][1000 genomes]
rs669046	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs670813	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs685844	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7245848	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7246684	0.82[ASN][1000 genomes]
rs7248700	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7249636	1.00[CEU][hapmap]
rs7254436	0.85[CHB][hapmap]
rs7254762	0.85[CHB][hapmap]
rs73025767	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8099863	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8103417	0.87[EUR][1000 genomes]
rs8105404	0.82[ASN][1000 genomes]
rs8105629	0.87[CEU][hapmap];1.00[JPT][hapmap]
rs8110470	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8111189	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8113558	0.87[CEU][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs8113738	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3385528	chr19:21030777-21495566	Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers 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	32 gene(s)	inside rSNPs	diseases
2	esv3518033	chr19:21278465-21747567	Strong transcription Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	esv3518034	chr19:21278465-21747567	ZNF genes & repeats Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	esv3414204	chr19:21301761-21839451	ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
5	nsv911415	chr19:21388995-21487170	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv911416	chr19:21388995-21548211	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	nsv911417	chr19:21388995-21564001	Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	nsv911419	chr19:21391844-21487170	Strong transcription Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	esv3325271	chr19:21445407-21792817	Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
10	nsv911420	chr19:21454672-21613397	ZNF genes & repeats Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
11	esv2751783	chr19:21465822-21726337	Strong transcription ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS 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	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs1678822	ZNF738	cis	Nerve Tibial	GTEx
rs1678822	CTD-2561J22.5	cis	Thyroid	GTEx
rs1678822	ZNF493	Cis_1M	lymphoblastoid	RTeQTL
rs1678822	ZNF738	cis	Esophagus Muscularis	GTEx
rs1678822	CTD-2561J22.5	cis	Adipose Subcutaneous	GTEx
rs1678822	ZNF738	cis	Adipose Subcutaneous	GTEx
rs1678822	ZNF738	Cis_1M	lymphoblastoid	RTeQTL
rs1678822	ZNF493	cis	multi-tissue	Pritchard
rs1678822	ZNF738	cis	Thyroid	GTEx

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21465000-21496000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr19:21465400-21484600	ZNF genes & repeats	Liver	Liver
3	chr19:21467200-21489600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr19:21470600-21484200	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
5	chr19:21471200-21479800	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
6	chr19:21471600-21479800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr19:21472000-21481800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr19:21472200-21487600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr19:21472200-21490400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr19:21473600-21479400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr19:21473600-21479600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr19:21473600-21487200	Weak transcription	Right Ventricle	heart
13	chr19:21473800-21479600	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
14	chr19:21473800-21510400	Weak transcription	Fetal Heart	heart
15	chr19:21474000-21479200	ZNF genes & repeats	Muscle Satellite Cultured Cells	--
16	chr19:21474000-21481600	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr19:21474000-21490600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
18	chr19:21474200-21479600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr19:21474200-21480800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr19:21474200-21482000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr19:21474400-21492400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr19:21474800-21509800	Weak transcription	Fetal Brain Male	brain
23	chr19:21475000-21480400	Weak transcription	Placenta	Placenta
24	chr19:21475200-21479800	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
25	chr19:21475200-21481800	Weak transcription	Pancreas	Pancrea
26	chr19:21475200-21481800	ZNF genes & repeats	Dnd41	blood
27	chr19:21475200-21483600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr19:21475200-21484000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr19:21475200-21484200	Weak transcription	Fetal Thymus	thymus
30	chr19:21475200-21485400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr19:21475200-21511200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr19:21475600-21479200	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
33	chr19:21475600-21479200	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
34	chr19:21475800-21479200	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
35	chr19:21475800-21480000	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr19:21475800-21481400	ZNF genes & repeats	Primary B cells from cord blood	blood
37	chr19:21476000-21479800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr19:21476000-21479800	ZNF genes & repeats	Duodenum Mucosa	Duodenum
39	chr19:21476000-21480800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
40	chr19:21476000-21481200	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr19:21476000-21482000	ZNF genes & repeats	Primary B cells from peripheral blood	blood
42	chr19:21476000-21490400	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
43	chr19:21476000-21490400	Weak transcription	Hela-S3	cervix
44	chr19:21476200-21479200	ZNF genes & repeats	Primary T killer memory cells from peripheral blood	blood
45	chr19:21476200-21479600	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
46	chr19:21476200-21488200	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr19:21476400-21479400	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
48	chr19:21476400-21479800	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
49	chr19:21476400-21480000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr19:21476400-21480000	ZNF genes & repeats	Fetal Intestine Large	intestine

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