Variant report

Variant	rs17244713
Chromosome Location	chr19:38050840-38050841
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 10 )

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

rs_ID	r²[population]
rs10445548	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1048505	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1061753	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1061756	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12151156	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17244769	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17303902	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17304703	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17305193	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17305228	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17305823	0.96[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17306900	0.86[ASN][1000 genomes]
rs1871196	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2291001	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2306201	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2385005	0.96[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35153242	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs502546	0.81[CEU][hapmap]
rs55681348	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55718806	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55743020	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55754546	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55865869	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55909413	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56277404	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56351266	0.86[ASN][1000 genomes]
rs57654288	0.95[EUR][1000 genomes]
rs57943942	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62108291	0.80[EUR][1000 genomes]
rs7245855	0.86[ASN][1000 genomes]
rs7259272	0.92[CEU][hapmap]
rs73031330	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73033122	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73033134	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73033142	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73035159	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73035160	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73039029	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73041006	0.86[ASN][1000 genomes]
rs8101610	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8104282	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8104994	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8108268	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8111790	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs17244713	AC012309.5	cis	Artery Tibial	GTEx
rs17244713	AC012309.5	cis	Esophagus Muscularis	GTEx
rs17244713	AC012309.5	cis	lung	GTEx
rs17244713	AC012309.5	cis	Esophagus Mucosa	GTEx
rs17244713	ZNF781	cis	Thyroid	GTEx
rs17244713	AC012309.5	cis	Thyroid	GTEx
rs17244713	ZNF585A	Cis_1M	lymphoblastoid	RTeQTL
rs17244713	AC012309.5	cis	Muscle Skeletal	GTEx
rs17244713	AC012309.5	cis	Heart Left Ventricle	GTEx
rs17244713	AC012309.5	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:27 , 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	chr19:38046400-38067200	ZNF genes & repeats	Brain Substantia Nigra	brain
10	chr19:38046400-38071800	ZNF genes & repeats	Brain Hippocampus Middle	brain
11	chr19:38046600-38053800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
12	chr19:38046600-38066800	ZNF genes & repeats	Duodenum Mucosa	Duodenum
13	chr19:38046600-38079600	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
14	chr19:38047000-38058600	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
15	chr19:38047400-38054800	ZNF genes & repeats	Brain Angular Gyrus	brain
16	chr19:38047400-38067000	ZNF genes & repeats	Brain Anterior Caudate	brain
17	chr19:38047400-38078600	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
18	chr19:38049200-38079600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
19	chr19:38050000-38057400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr19:38050200-38051200	Weak transcription	Ovary	ovary
21	chr19:38050200-38051200	Weak transcription	Small Intestine	intestine
22	chr19:38050200-38051400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr19:38050200-38051400	Weak transcription	Aorta	Aorta
24	chr19:38050200-38051400	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr19:38050200-38055400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr19:38050600-38051400	Weak transcription	Fetal Lung	lung
27	chr19:38050800-38052200	ZNF genes & repeats	Fetal Stomach	stomach

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