Variant report

Variant	rs12974840
Chromosome Location	chr19:53013294-53013295
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10582148	0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11667348	0.95[ASN][1000 genomes]
rs11668903	0.92[ASN][1000 genomes]
rs12462347	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12463002	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12610240	0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12982862	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12984325	0.80[ASN][1000 genomes]
rs162277	0.84[EUR][1000 genomes]
rs162278	0.85[EUR][1000 genomes]
rs172955	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2115372	0.87[ASN][1000 genomes]
rs2608522	0.83[EUR][1000 genomes]
rs2868688	0.86[ASN][1000 genomes]
rs326458	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34222822	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs36039960	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs376595	0.83[EUR][1000 genomes]
rs396663	0.80[EUR][1000 genomes]
rs400709	0.82[EUR][1000 genomes]
rs410046	0.85[EUR][1000 genomes]
rs413751	0.85[EUR][1000 genomes]
rs413814	0.82[EUR][1000 genomes]
rs417599	0.83[EUR][1000 genomes]
rs422195	0.81[EUR][1000 genomes]
rs429367	0.84[EUR][1000 genomes]
rs434709	0.83[EUR][1000 genomes]
rs439618	0.82[EUR][1000 genomes]
rs440545	0.84[EUR][1000 genomes]
rs441850	0.84[EUR][1000 genomes]
rs445500	0.84[EUR][1000 genomes]
rs449671	0.84[EUR][1000 genomes]
rs4802964	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4802965	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4802966	0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4802967	0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4802972	0.83[EUR][1000 genomes]
rs490663	0.97[ASN][1000 genomes]
rs62119356	0.87[ASN][1000 genomes]
rs688646	0.84[EUR][1000 genomes]
rs7257823	0.93[ASN][1000 genomes]
rs8101346	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[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:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:53002200-53014200	ZNF genes & repeats	Ovary	ovary
2	chr19:53002600-53021400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr19:53003000-53014800	Weak transcription	Brain Germinal Matrix	brain
4	chr19:53003400-53022600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr19:53003800-53015000	Weak transcription	Fetal Lung	lung
6	chr19:53003800-53017600	Weak transcription	Fetal Muscle Trunk	muscle
7	chr19:53004400-53014800	Weak transcription	Brain Angular Gyrus	brain
8	chr19:53004600-53014600	Weak transcription	Fetal Brain Male	brain
9	chr19:53004600-53015800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr19:53005400-53015800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
11	chr19:53005800-53014000	Weak transcription	Dnd41	blood
12	chr19:53006400-53021200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr19:53006400-53021400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr19:53006600-53014400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr19:53006600-53014800	Weak transcription	Brain Anterior Caudate	brain
16	chr19:53006600-53015600	Strong transcription	Cortex derived primary cultured neurospheres	brain
17	chr19:53006600-53016200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr19:53006800-53015000	Weak transcription	Fetal Brain Female	brain
19	chr19:53006800-53021400	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr19:53007000-53015000	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr19:53007000-53021400	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr19:53007400-53015200	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr19:53008400-53015600	Strong transcription	HUES6 Cell Line	embryonic stem cell
24	chr19:53009000-53022600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr19:53009400-53014000	Weak transcription	Brain Hippocampus Middle	brain
26	chr19:53009600-53013800	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr19:53009600-53013800	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr19:53009800-53014000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr19:53010000-53014800	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr19:53010800-53013800	Weak transcription	Fetal Muscle Leg	muscle
31	chr19:53011000-53013400	Weak transcription	Stomach Smooth Muscle	stomach
32	chr19:53011000-53017800	Weak transcription	Right Ventricle	heart
33	chr19:53012200-53016000	ZNF genes & repeats	Adipose Nuclei	Adipose
34	chr19:53012400-53014000	Weak transcription	Fetal Kidney	kidney
35	chr19:53012400-53015200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr19:53012400-53016200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr19:53012600-53015800	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr19:53012800-53015600	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr19:53013000-53013600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr19:53013000-53013800	Weak transcription	Aorta	Aorta
41	chr19:53013000-53013800	Weak transcription	Left Ventricle	heart
42	chr19:53013000-53016000	Weak transcription	Rectal Smooth Muscle	rectum
43	chr19:53013000-53016200	Weak transcription	Brain Cingulate Gyrus	brain
44	chr19:53013000-53016200	Weak transcription	Fetal Stomach	stomach
45	chr19:53013200-53015000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr19:53013200-53015200	Strong transcription	HSMMtube	muscle
47	chr19:53013200-53021800	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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