Variant report

Variant	rs7247090
Chromosome Location	chr19:38013411-38013412
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1019494	0.91[ASN][1000 genomes]
rs10419281	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11083423	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11666708	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12462546	0.91[ASN][1000 genomes]
rs12981359	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12981830	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1545755	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1968251	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2385180	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2385181	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34410821	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35470250	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35864326	0.82[EUR][1000 genomes]
rs4344867	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6508721	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6508725	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7254009	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8109103	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv918028	chr19:37020645-38014526	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Strong transcription 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 miRNA target site	73 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	nsv1056753	chr19:37963714-38015943	Weak transcription Active TSS Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7247090	ZNF585A	Cis_1M	lymphoblastoid	RTeQTL
rs7247090	AC012309.5	cis	Artery Tibial	GTEx
rs7247090	AC012309.5	cis	Thyroid	GTEx
rs7247090	AC012309.5	cis	Esophagus Muscularis	GTEx
rs7247090	AC012309.5	cis	Heart Left Ventricle	GTEx

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37998800-38014000	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr19:37998800-38021000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr19:37998800-38022600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr19:37999000-38013800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr19:37999000-38028800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr19:37999200-38018400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr19:38002000-38028800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
8	chr19:38006000-38020800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr19:38007400-38013600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr19:38008800-38026600	Weak transcription	Fetal Heart	heart
11	chr19:38009400-38020000	ZNF genes & repeats	Fetal Intestine Small	intestine
12	chr19:38010600-38018400	Strong transcription	Fetal Brain Female	brain
13	chr19:38010600-38020600	Strong transcription	Fetal Muscle Leg	muscle
14	chr19:38010800-38020400	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
15	chr19:38010800-38020800	Strong transcription	Brain Anterior Caudate	brain
16	chr19:38011000-38020800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
17	chr19:38011600-38014000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr19:38011600-38014000	Weak transcription	Thymus	Thymus
19	chr19:38011600-38023600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr19:38011800-38013600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr19:38011800-38013600	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr19:38011800-38013600	Weak transcription	Right Ventricle	heart
23	chr19:38011800-38014000	Weak transcription	NHEK	skin
24	chr19:38011800-38016600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr19:38012400-38013800	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr19:38012800-38013800	ZNF genes & repeats	Stomach Smooth Muscle	stomach
27	chr19:38012800-38014400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr19:38012800-38014400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
29	chr19:38012800-38014800	Strong transcription	Fetal Brain Male	brain
30	chr19:38012800-38020800	Strong transcription	Fetal Muscle Trunk	muscle
31	chr19:38013000-38013600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
32	chr19:38013000-38013600	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
33	chr19:38013000-38013600	ZNF genes & repeats	Brain Hippocampus Middle	brain
34	chr19:38013000-38014000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr19:38013000-38014600	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
36	chr19:38013000-38014600	ZNF genes & repeats	Small Intestine	intestine
37	chr19:38013000-38014800	ZNF genes & repeats	Adipose Nuclei	Adipose
38	chr19:38013000-38015600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr19:38013000-38015800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr19:38013000-38015800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr19:38013000-38016000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
42	chr19:38013000-38017600	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
43	chr19:38013000-38017800	ZNF genes & repeats	Ovary	ovary
44	chr19:38013200-38014200	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr19:38013200-38014200	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
46	chr19:38013200-38014600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr19:38013200-38014600	ZNF genes & repeats	Primary T helper 17 cells PMA-I stimulated	--
48	chr19:38013200-38014800	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
49	chr19:38013200-38015000	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr19:38013200-38015600	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon

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