Variant report

Variant	rs1993531
Chromosome Location	chr19:52884886-52884887
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10445583	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10445584	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10445585	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1054612	0.86[EUR][1000 genomes]
rs11084150	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11084151	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11084152	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11084153	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11084154	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11084155	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11084156	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11084157	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1993530	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2042913	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2059817	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2059818	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2062971	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3170100	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34221182	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4802926	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55748277	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56151179	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60935857	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62108317	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62108318	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62108319	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62108320	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62108321	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8104808	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8104812	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065410	chr19:52103914-52889530	Genic enhancers Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS 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 miRNA target site	596 gene(s)	inside rSNPs	diseases
2	nsv1066015	chr19:52502213-52890308	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv544059	chr19:52502213-52890308	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv833873	chr19:52788939-52937281	Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv1066537	chr19:52794424-53044977	Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic 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	24 gene(s)	inside rSNPs	diseases
6	nsv544060	chr19:52794424-53044977	ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
7	esv3401193	chr19:52818960-52909749	ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Genic 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	16 gene(s)	inside rSNPs	diseases
8	nsv912300	chr19:52832830-52928039	Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
9	nsv912301	chr19:52835210-52914233	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
10	nsv912302	chr19:52859828-52928039	Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
11	nsv2536	chr19:52869457-52902064	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
12	nsv912303	chr19:52874140-52928039	ZNF genes & repeats Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
13	esv3372061	chr19:52877189-52902218	Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
14	esv2750580	chr19:52882430-52885223	Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1993531	LOC400713	Cis_1M	lymphoblastoid	RTeQTL
rs1993531	ZNF880	cis	Esophagus Muscularis	GTEx
rs1993531	ZNF880	cis	Nerve Tibial	GTEx
rs1993531	ZNF880	cis	Artery Tibial	GTEx
rs1993531	ZNF880	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52873600-52888400	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
2	chr19:52873800-52885000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
3	chr19:52874000-52887200	ZNF genes & repeats	Fetal Intestine Large	intestine
4	chr19:52874200-52886200	Weak transcription	HUVEC	blood vessel
5	chr19:52874200-52886800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr19:52875600-52888600	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
7	chr19:52876200-52886200	Strong transcription	Placenta Amnion	Placenta Amnion
8	chr19:52876200-52886600	Strong transcription	Skeletal Muscle Male	skeletal muscle
9	chr19:52876200-52888400	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
10	chr19:52876200-52888800	ZNF genes & repeats	Primary T cells from cord blood	blood
11	chr19:52876200-52889000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
12	chr19:52876200-52889000	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
13	chr19:52876200-52889000	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
14	chr19:52876200-52889600	ZNF genes & repeats	Fetal Kidney	kidney
15	chr19:52876200-52889800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr19:52876200-52889800	ZNF genes & repeats	Fetal Brain Female	brain
17	chr19:52876200-52890000	ZNF genes & repeats	Ovary	ovary
18	chr19:52876200-52890600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr19:52876200-52890600	ZNF genes & repeats	Fetal Lung	lung
20	chr19:52876200-52890800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr19:52876200-52890800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
22	chr19:52876200-52890800	ZNF genes & repeats	Liver	Liver
23	chr19:52876200-52893400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
24	chr19:52876200-52893800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr19:52876200-52894000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr19:52876200-52894000	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr19:52876200-52894200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr19:52876200-52895000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
29	chr19:52876400-52885600	ZNF genes & repeats	Fetal Stomach	stomach
30	chr19:52876400-52885800	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
31	chr19:52876400-52886800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr19:52876400-52888000	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
33	chr19:52876400-52890600	ZNF genes & repeats	Primary B cells from peripheral blood	blood
34	chr19:52876400-52891000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr19:52877000-52885600	ZNF genes & repeats	Fetal Intestine Small	intestine
36	chr19:52877400-52893800	ZNF genes & repeats	Duodenum Mucosa	Duodenum
37	chr19:52877600-52885600	ZNF genes & repeats	Aorta	Aorta
38	chr19:52877800-52889800	ZNF genes & repeats	Fetal Muscle Leg	muscle
39	chr19:52877800-52894200	ZNF genes & repeats	Adipose Nuclei	Adipose
40	chr19:52879000-52888800	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
41	chr19:52879000-52889000	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr19:52879000-52889800	ZNF genes & repeats	Primary B cells from cord blood	blood
43	chr19:52879000-52889800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr19:52879000-52890600	ZNF genes & repeats	Colon Smooth Muscle	Colon
45	chr19:52879600-52890400	ZNF genes & repeats	Brain Germinal Matrix	brain
46	chr19:52880200-52889000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr19:52880200-52889200	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
48	chr19:52880200-52890600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr19:52880400-52893800	ZNF genes & repeats	Fetal Muscle Trunk	muscle
50	chr19:52880600-52885600	ZNF genes & repeats	Placenta	Placenta

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