Variant report

Variant	rs73031330
Chromosome Location	chr19:38048804-38048805
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10445548	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1048505	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1061753	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1061756	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12151156	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17244713	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17244769	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17303902	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17304703	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17305193	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17305228	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17305823	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17306900	0.86[ASN][1000 genomes]
rs1871196	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2291001	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2306201	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2385005	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35153242	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55681348	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55718806	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55743020	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55754546	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55865869	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55909413	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56277404	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56351266	0.86[ASN][1000 genomes]
rs57654288	0.97[EUR][1000 genomes]
rs57943942	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62108291	0.82[EUR][1000 genomes]
rs62108306	0.80[EUR][1000 genomes]
rs7245855	0.86[ASN][1000 genomes]
rs7259272	0.80[EUR][1000 genomes]
rs73033122	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73033134	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73033142	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73035159	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73035160	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73039029	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73041006	0.86[ASN][1000 genomes]
rs8101610	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8104282	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8104994	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8108268	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8111790	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757695	chr19:37794850-38051606	Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	esv2758759	chr19:37794850-38051606	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv833819	chr19:37899501-38051599	ZNF genes & repeats Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv579468	chr19:37977609-38293487	ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS 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 target site	58 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs73031330	AC012309.5	cis	Esophagus Muscularis	GTEx
rs73031330	AC012309.5	cis	Skin Sun Exposed Lower leg	GTEx
rs73031330	AC012309.5	cis	Esophagus Mucosa	GTEx
rs73031330	AC012309.5	cis	Muscle Skeletal	GTEx
rs73031330	AC012309.5	cis	Heart Left Ventricle	GTEx
rs73031330	AC012309.5	cis	Thyroid	GTEx
rs73031330	AC012309.5	cis	lung	GTEx
rs73031330	ZNF781	cis	Thyroid	GTEx
rs73031330	AC012309.5	cis	Artery Tibial	GTEx

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38032400-38080800	ZNF genes & repeats	Liver	Liver
2	chr19:38032600-38075200	ZNF genes & repeats	Adipose Nuclei	Adipose
3	chr19:38038000-38078400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr19:38038600-38079600	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
5	chr19:38041200-38079600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr19:38041800-38059600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr19:38042800-38053800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr19:38045000-38078600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr19:38046400-38050000	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr19:38046400-38050400	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr19:38046400-38067200	ZNF genes & repeats	Brain Substantia Nigra	brain
12	chr19:38046400-38071800	ZNF genes & repeats	Brain Hippocampus Middle	brain
13	chr19:38046600-38050200	ZNF genes & repeats	Brain Dorsolateral Prefrontal Cortex	brain
14	chr19:38046600-38050400	ZNF genes & repeats	Fetal Brain Female	brain
15	chr19:38046600-38053800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
16	chr19:38046600-38066800	ZNF genes & repeats	Duodenum Mucosa	Duodenum
17	chr19:38046600-38079600	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
18	chr19:38046800-38050000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
19	chr19:38046800-38050200	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr19:38046800-38050200	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr19:38046800-38050200	ZNF genes & repeats	Fetal Muscle Leg	muscle
22	chr19:38046800-38050200	ZNF genes & repeats	Ovary	ovary
23	chr19:38046800-38050200	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
24	chr19:38046800-38050800	ZNF genes & repeats	Stomach Smooth Muscle	stomach
25	chr19:38047000-38050200	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr19:38047000-38050200	ZNF genes & repeats	Fetal Stomach	stomach
27	chr19:38047000-38050400	ZNF genes & repeats	Brain Cingulate Gyrus	brain
28	chr19:38047000-38050600	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
29	chr19:38047000-38050800	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
30	chr19:38047000-38058600	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
31	chr19:38047200-38050200	ZNF genes & repeats	Left Ventricle	heart
32	chr19:38047200-38050600	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
33	chr19:38047400-38049000	ZNF genes & repeats	Brain Germinal Matrix	brain
34	chr19:38047400-38050200	ZNF genes & repeats	Colon Smooth Muscle	Colon
35	chr19:38047400-38050400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr19:38047400-38050600	ZNF genes & repeats	Fetal Lung	lung
37	chr19:38047400-38054800	ZNF genes & repeats	Brain Angular Gyrus	brain
38	chr19:38047400-38067000	ZNF genes & repeats	Brain Anterior Caudate	brain
39	chr19:38047400-38078600	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
40	chr19:38047600-38050200	ZNF genes & repeats	Pancreas	Pancrea
41	chr19:38047600-38050400	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
42	chr19:38047800-38050200	ZNF genes & repeats	Aorta	Aorta
43	chr19:38048000-38050000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr19:38048000-38050800	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr19:38048200-38049800	ZNF genes & repeats	Placenta	Placenta
46	chr19:38048200-38050200	ZNF genes & repeats	Rectal Smooth Muscle	rectum
47	chr19:38048600-38049000	ZNF genes & repeats	Primary T killer memory cells from peripheral blood	blood
48	chr19:38048600-38050600	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum

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