Variant report

Variant	rs7254009
Chromosome Location	chr19:37918609-37918610
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1019494	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10419281	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10421436	0.82[EUR][1000 genomes]
rs10425719	0.92[CEU][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes]
rs11083423	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11666708	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12462546	0.91[ASN][1000 genomes]
rs12981359	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12981830	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1545755	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs185368	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs185369	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1968251	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2291001	0.82[ASW][hapmap]
rs2306201	0.82[ASW][hapmap]
rs2385180	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2385181	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2431992	0.90[CHD][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs256733	0.82[ASW][hapmap];1.00[CEU][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs256735	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs256740	0.84[ASN][1000 genomes]
rs256744	0.84[ASN][1000 genomes]
rs320881	0.83[CHD][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap]
rs34410821	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35470250	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4344867	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs502546	0.86[JPT][hapmap]
rs55755939	0.82[ASN][1000 genomes]
rs6508721	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6508725	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7247090	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8109103	0.82[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs862234	1.00[ASW][hapmap];0.81[CHD][hapmap];0.83[JPT][hapmap];0.82[YRI][hapmap]

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	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	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:14)

SNP	Gene	Cis/trans	Tissue	Source
rs7254009	DMPK	cis	parietal	SCAN
rs7254009	AC012309.5	cis	Thyroid	GTEx
rs7254009	CBLC	cis	parietal	SCAN
rs7254009	AC012309.5	cis	Artery Tibial	GTEx
rs7254009	PHLDB3	cis	cerebellum	SCAN
rs7254009	AC012309.5	cis	Heart Left Ventricle	GTEx
rs7254009	AC012309.5	cis	Esophagus Muscularis	GTEx
rs7254009	AKT2	cis	parietal	SCAN
rs7254009	HIPK4	cis	parietal	SCAN
rs7254009	PLEKHG2	cis	cerebellum	SCAN
rs7254009	ZNF585A	Cis_1M	lymphoblastoid	RTeQTL
rs7254009	IL29	cis	parietal	SCAN
rs7254009	ZNF226	cis	cerebellum	SCAN
rs7254009	EIF3K	cis	parietal	SCAN

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37898000-37927000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr19:37898000-37956400	ZNF genes & repeats	Liver	Liver
3	chr19:37899200-37918800	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr19:37900200-37927000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr19:37903200-37925000	ZNF genes & repeats	Primary T cells from cord blood	blood
6	chr19:37903200-37927200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr19:37903200-37936600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr19:37903400-37936400	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
9	chr19:37906800-37927000	ZNF genes & repeats	Fetal Brain Female	brain
10	chr19:37906800-37936600	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
11	chr19:37907600-37925000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
12	chr19:37907600-37926600	ZNF genes & repeats	Primary B cells from peripheral blood	blood
13	chr19:37907800-37926000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
14	chr19:37909200-37919400	ZNF genes & repeats	Fetal Lung	lung
15	chr19:37910600-37925000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
16	chr19:37910800-37956000	ZNF genes & repeats	Adipose Nuclei	Adipose
17	chr19:37911000-37926400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
18	chr19:37911000-37927000	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
19	chr19:37911200-37919000	ZNF genes & repeats	Brain Hippocampus Middle	brain
20	chr19:37911200-37925000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr19:37911200-37926600	ZNF genes & repeats	Brain Substantia Nigra	brain
22	chr19:37911200-37927000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
23	chr19:37911200-37927000	ZNF genes & repeats	Dnd41	blood
24	chr19:37911200-37936600	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
25	chr19:37911200-37936600	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
26	chr19:37911200-37954600	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
27	chr19:37911400-37919000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr19:37911400-37919200	ZNF genes & repeats	Primary T helper 17 cells PMA-I stimulated	--
29	chr19:37911400-37919400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr19:37911400-37923000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
31	chr19:37911400-37925600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr19:37912000-37925000	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
33	chr19:37914600-37921600	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
34	chr19:37914600-37925200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr19:37914800-37927000	ZNF genes & repeats	Brain Germinal Matrix	brain
36	chr19:37915000-37918800	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
37	chr19:37915000-37920800	ZNF genes & repeats	Fetal Muscle Leg	muscle
38	chr19:37915000-37926600	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
39	chr19:37915200-37920600	ZNF genes & repeats	Thymus	Thymus
40	chr19:37915200-37924200	ZNF genes & repeats	Left Ventricle	heart
41	chr19:37915200-37925800	ZNF genes & repeats	Ovary	ovary
42	chr19:37915200-37926000	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr19:37915400-37919400	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr19:37915400-37926000	ZNF genes & repeats	Fetal Stomach	stomach
45	chr19:37915600-37925000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr19:37915800-37918800	ZNF genes & repeats	Fetal Muscle Trunk	muscle
47	chr19:37915800-37919400	ZNF genes & repeats	Rectal Smooth Muscle	rectum
48	chr19:37915800-37923000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
49	chr19:37915800-37924200	ZNF genes & repeats	Aorta	Aorta
50	chr19:37915800-37926000	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood

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