Variant report

Variant	rs6508721
Chromosome Location	chr19:37910021-37910022
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1019494	0.94[ASN][1000 genomes]
rs10419281	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10421436	0.83[EUR][1000 genomes]
rs10425719	0.82[EUR][1000 genomes]
rs11083423	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11666708	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12462546	0.88[ASN][1000 genomes]
rs12981359	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12981830	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1545755	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs185368	0.84[AFR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs185369	0.84[AFR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1968251	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2385180	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2385181	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2431992	0.84[ASN][1000 genomes]
rs256733	0.84[AFR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs256735	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs256740	0.87[ASN][1000 genomes]
rs256744	0.87[ASN][1000 genomes]
rs34410821	0.84[AFR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35470250	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4344867	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55755939	0.84[ASN][1000 genomes]
rs6508725	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7247090	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7254009	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73025481	0.82[ASN][1000 genomes]
rs8109103	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv1057688	chr19:37828019-37988253	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv579465	chr19:37868552-37917692	ZNF genes & repeats Strong transcription Weak transcription Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
6	nsv963044	chr19:37893588-37916743	ZNF genes & repeats Weak transcription Strong transcription Active TSS	lncRNA	n/a	inside rSNPs	diseases
7	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6508721	AC012309.5	cis	Esophagus Muscularis	GTEx
rs6508721	AC012309.5	cis	Thyroid	GTEx
rs6508721	ZNF585A	Cis_1M	lymphoblastoid	RTeQTL
rs6508721	AC012309.5	cis	Artery Tibial	GTEx
rs6508721	AC012309.5	cis	Heart Left Ventricle	GTEx

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37898000-37910400	ZNF genes & repeats	Adipose Nuclei	Adipose
2	chr19:37898000-37927000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr19:37898000-37956400	ZNF genes & repeats	Liver	Liver
4	chr19:37899200-37918800	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr19:37900200-37927000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr19:37903000-37910200	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
7	chr19:37903000-37910200	ZNF genes & repeats	Dnd41	blood
8	chr19:37903200-37925000	ZNF genes & repeats	Primary T cells from cord blood	blood
9	chr19:37903200-37927200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr19:37903200-37936600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr19:37903400-37936400	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
12	chr19:37905200-37913000	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr19:37906400-37913000	ZNF genes & repeats	Aorta	Aorta
14	chr19:37906400-37914000	ZNF genes & repeats	Left Ventricle	heart
15	chr19:37906600-37913800	ZNF genes & repeats	Ovary	ovary
16	chr19:37906600-37913800	ZNF genes & repeats	Psoas Muscle	Psoas
17	chr19:37906800-37910600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
18	chr19:37906800-37915400	ZNF genes & repeats	Duodenum Mucosa	Duodenum
19	chr19:37906800-37918000	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr19:37906800-37927000	ZNF genes & repeats	Fetal Brain Female	brain
21	chr19:37906800-37936600	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
22	chr19:37907000-37910200	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
23	chr19:37907000-37910400	ZNF genes & repeats	Primary B cells from cord blood	blood
24	chr19:37907600-37925000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
25	chr19:37907600-37926600	ZNF genes & repeats	Primary B cells from peripheral blood	blood
26	chr19:37907800-37915600	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
27	chr19:37907800-37926000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
28	chr19:37908000-37913800	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
29	chr19:37908400-37910400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr19:37908400-37911200	Weak transcription	HSMMtube	muscle
31	chr19:37908600-37911400	Weak transcription	Thymus	Thymus
32	chr19:37908800-37911200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr19:37909200-37910200	ZNF genes & repeats	Fetal Brain Male	brain
34	chr19:37909200-37910200	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
35	chr19:37909200-37919400	ZNF genes & repeats	Fetal Lung	lung
36	chr19:37909600-37911400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr19:37909800-37911200	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr19:37909800-37911200	Weak transcription	Rectal Smooth Muscle	rectum
39	chr19:37909800-37911400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr19:37909800-37911400	Weak transcription	Right Ventricle	heart
41	chr19:37909800-37911800	Weak transcription	Pancreas	Pancrea
42	chr19:37910000-37911000	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr19:37910000-37911200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr19:37910000-37911200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr19:37910000-37911200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr19:37910000-37911200	Weak transcription	Brain Cingulate Gyrus	brain
47	chr19:37910000-37911200	Weak transcription	Brain Hippocampus Middle	brain
48	chr19:37910000-37911200	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr19:37910000-37911200	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr19:37910000-37911200	Weak transcription	Stomach Smooth Muscle	stomach

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