Variant report

Variant	rs389503
Chromosome Location	chr19:53008367-53008368
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11084170	0.84[ASN][1000 genomes]
rs11669969	0.83[ASN][1000 genomes]
rs12610532	0.90[ASN][1000 genomes]
rs12984325	0.84[ASN][1000 genomes]
rs161932	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1677467	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs172956	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2011702	0.83[ASN][1000 genomes]
rs324745	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs324747	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs324748	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs326452	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs326456	0.86[EUR][1000 genomes]
rs329929	0.81[ASN][1000 genomes]
rs329930	0.82[ASN][1000 genomes]
rs378790	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs400278	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs414595	0.94[ASN][1000 genomes]
rs414804	0.84[ASN][1000 genomes]
rs419317	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4802968	0.90[ASN][1000 genomes]
rs4802969	0.86[ASN][1000 genomes]
rs4802970	0.90[ASN][1000 genomes]
rs621469	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs633763	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs650885	0.86[ASN][1000 genomes]
rs650937	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs802878	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1066537	chr19:52794424-53044977	Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS 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	24 gene(s)	inside rSNPs	diseases
2	nsv544060	chr19:52794424-53044977	ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv580026	chr19:52937100-53059872	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1063648	chr19:52938131-53041119	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1057296	chr19:52950339-53396986	Weak transcription Active TSS ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
6	nsv978841	chr19:52983057-53088237	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	esv3404701	chr19:52986895-53035152	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv1058567	chr19:52992455-53021505	Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Active TSS Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	diseases
9	esv3440535	chr19:52993529-53035203	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv1066717	chr19:52993620-53041995	Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv1064342	chr19:52996710-53041119	ZNF genes & repeats Active TSS Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv1055825	chr19:53001299-53037378	Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	nsv1055859	chr19:53001299-53041119	Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
14	nsv1060656	chr19:53001299-53041995	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52997600-53009800	Weak transcription	Rectal Smooth Muscle	rectum
2	chr19:53002200-53014200	ZNF genes & repeats	Ovary	ovary
3	chr19:53002600-53021400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr19:53002800-53010600	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr19:53003000-53014800	Weak transcription	Brain Germinal Matrix	brain
6	chr19:53003200-53009600	Weak transcription	Brain Cingulate Gyrus	brain
7	chr19:53003400-53022600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr19:53003800-53015000	Weak transcription	Fetal Lung	lung
9	chr19:53003800-53017600	Weak transcription	Fetal Muscle Trunk	muscle
10	chr19:53004000-53009400	ZNF genes & repeats	Lung	lung
11	chr19:53004400-53013000	Strong transcription	Fetal Stomach	stomach
12	chr19:53004400-53014800	Weak transcription	Brain Angular Gyrus	brain
13	chr19:53004600-53014600	Weak transcription	Fetal Brain Male	brain
14	chr19:53004600-53015800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr19:53004800-53011000	Strong transcription	Right Ventricle	heart
16	chr19:53004800-53012800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr19:53005200-53009000	Weak transcription	HSMMtube	muscle
18	chr19:53005200-53009200	ZNF genes & repeats	Spleen	Spleen
19	chr19:53005200-53009400	ZNF genes & repeats	Adipose Nuclei	Adipose
20	chr19:53005200-53010000	Strong transcription	Stomach Smooth Muscle	stomach
21	chr19:53005400-53008400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr19:53005400-53015800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
23	chr19:53005600-53010800	ZNF genes & repeats	Left Ventricle	heart
24	chr19:53005800-53010800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr19:53005800-53014000	Weak transcription	Dnd41	blood
26	chr19:53006400-53009000	Weak transcription	Brain Hippocampus Middle	brain
27	chr19:53006400-53021200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr19:53006400-53021400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr19:53006600-53009200	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr19:53006600-53009400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr19:53006600-53009600	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr19:53006600-53014400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr19:53006600-53014800	Weak transcription	Brain Anterior Caudate	brain
34	chr19:53006600-53015600	Strong transcription	Cortex derived primary cultured neurospheres	brain
35	chr19:53006600-53016200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr19:53006800-53015000	Weak transcription	Fetal Brain Female	brain
37	chr19:53006800-53021400	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr19:53007000-53015000	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr19:53007000-53021400	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr19:53007200-53009200	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr19:53007400-53009000	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr19:53007400-53015200	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr19:53007600-53008400	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr19:53007600-53008400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr19:53007600-53008800	Weak transcription	Aorta	Aorta
46	chr19:53007600-53010400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr19:53008000-53009000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr19:53008200-53008800	Weak transcription	Fetal Muscle Leg	muscle
49	chr19:53008200-53010400	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr19:53008200-53011600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland

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