Variant report

Variant	rs4359573
Chromosome Location	chr19:21542296-21542297
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 105 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs10414834	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10424079	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11666213	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11666447	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11666525	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11666540	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11667103	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11667361	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11667392	0.82[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11669033	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11669790	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11670815	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11670868	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11672341	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11672583	1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11673320	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11879901	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13346641	0.81[CEU][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1621154	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1626404	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1762578	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17680605	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1781867	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1781872	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1967182	0.86[CEU][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2061916	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2154302	0.96[EUR][1000 genomes]
rs2358993	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2359144	0.85[CEU][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2359145	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2562405	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2562411	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2562413	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2562416	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2562456	0.95[CEU][hapmap]
rs2650776	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2650793	0.95[CEU][hapmap]
rs2650805	1.00[CEU][hapmap]
rs2650844	0.84[CEU][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2650848	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs279807	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs279809	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2914646	0.84[AFR][1000 genomes]
rs2928211	0.81[EUR][1000 genomes]
rs3853837	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3853838	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4321312	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4327181	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4544364	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4638726	0.85[CEU][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs55756795	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs55790393	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs55875743	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55899865	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57299552	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58412280	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs60173523	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61035285	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62107465	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62107468	0.87[EUR][1000 genomes]
rs62107469	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62107472	0.97[EUR][1000 genomes]
rs62107479	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62107531	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62107532	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62107534	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62107536	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62107539	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62107540	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62107541	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62109225	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62109226	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62109227	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62109228	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62109229	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62110071	0.82[AFR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62110367	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62110377	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62110416	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62110420	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62110424	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62110426	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62110427	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62110428	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62110429	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs627522	1.00[CEU][hapmap]
rs6511253	1.00[CEU][hapmap]
rs7246339	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7251135	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7258099	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7258473	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7258562	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7260065	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs73537884	0.83[AMR][1000 genomes];0.99[EUR][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	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	esv3363678	chr19:21483148-21756908	Strong transcription Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Enhancers 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	31 gene(s)	inside rSNPs	diseases
10	nsv963023	chr19:21491992-21570395	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	nsv578952	chr19:21535707-21868584	Genic enhancers Active TSS ZNF genes & repeats Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4359573	RP11-678G14.2	cis	Esophagus Muscularis	GTEx
rs4359573	ZNF708	cis	lung	GTEx
rs4359573	ZNF708	cis	Muscle Skeletal	GTEx
rs4359573	RP11-678G14.3	cis	Adipose Subcutaneous	GTEx
rs4359573	ZNF708	cis	Skin Sun Exposed Lower leg	GTEx
rs4359573	RP11-678G14.2	cis	Whole Blood	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21541200-21543000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr19:21541400-21542400	Bivalent/Poised TSS	Brain Germinal Matrix	brain
3	chr19:21541400-21542400	Active TSS	Brain Substantia Nigra	brain
4	chr19:21541400-21542400	Active TSS	Colon Smooth Muscle	Colon
5	chr19:21541400-21542400	Active TSS	Fetal Muscle Trunk	muscle
6	chr19:21541400-21542400	Active TSS	A549	lung
7	chr19:21541400-21542600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr19:21541400-21542600	Active TSS	Primary T helper cells PMA-I stimulated	--
9	chr19:21541400-21542600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
10	chr19:21541400-21542600	Active TSS	Cortex derived primary cultured neurospheres	brain
11	chr19:21541400-21542600	Active TSS	Brain Anterior Caudate	brain
12	chr19:21541400-21542600	Active TSS	Brain Hippocampus Middle	brain
13	chr19:21541400-21542600	Active TSS	Brain Inferior Temporal Lobe	brain
14	chr19:21541400-21542600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
15	chr19:21541400-21542600	Active TSS	Rectal Smooth Muscle	rectum
16	chr19:21541400-21542600	Active TSS	Skeletal Muscle Male	skeletal muscle
17	chr19:21541400-21542600	Active TSS	Stomach Smooth Muscle	stomach
18	chr19:21541400-21542600	Active TSS	Monocytes-CD14+_RO01746	blood
19	chr19:21541400-21542800	Active TSS	Primary T cells from cord blood	blood
20	chr19:21541400-21542800	Active TSS	Primary hematopoietic stem cells	blood
21	chr19:21541400-21542800	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr19:21541400-21542800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr19:21541400-21542800	Active TSS	Duodenum Smooth Muscle	Duodenum
24	chr19:21541400-21542800	Active TSS	Fetal Brain Male	brain
25	chr19:21541400-21542800	Active TSS	Fetal Intestine Large	intestine
26	chr19:21541400-21542800	Active TSS	Fetal Intestine Small	intestine
27	chr19:21541400-21542800	Active TSS	Ovary	ovary
28	chr19:21541400-21542800	Active TSS	HSMMtube	muscle
29	chr19:21541400-21543000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr19:21541400-21543000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr19:21541400-21543000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr19:21541400-21543000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr19:21541400-21543000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr19:21541400-21543000	Active TSS	Primary hematopoietic stem cells short term culture	blood
35	chr19:21541400-21543000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr19:21541400-21543000	Active TSS	Muscle Satellite Cultured Cells	--
37	chr19:21541400-21543000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr19:21541400-21543000	Active TSS	Duodenum Mucosa	Duodenum
39	chr19:21541400-21543000	Active TSS	Thymus	Thymus
40	chr19:21541400-21543000	Active TSS	HUVEC	blood vessel
41	chr19:21541400-21543000	Active TSS	NHDF-Ad	bronchial
42	chr19:21541400-21543000	Active TSS	NHLF	lung
43	chr19:21541400-21543200	Active TSS	ES-I3 Cell Line	embryonic stem cell
44	chr19:21541400-21543200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr19:21541400-21543200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr19:21541400-21543200	Active TSS	HUES6 Cell Line	embryonic stem cell
47	chr19:21541400-21543200	Active TSS	HUES64 Cell Line	embryonic stem cell
48	chr19:21541400-21543200	Active TSS	Fetal Kidney	kidney
49	chr19:21541400-21543200	Active TSS	Rectal Mucosa Donor 29	rectum
50	chr19:21541400-21543200	Active TSS	Rectal Mucosa Donor 31	rectum

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