Variant report

Variant	rs13343485
Chromosome Location	chr19:37874281-37874282
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF569-3	chr19:37874109-37874614	l_1679_chr19:37869793-37874605_adrenal

Extended variants
information (count: 114 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs1015848	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1015849	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1035479	0.90[EUR][1000 genomes]
rs10403582	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10403613	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10404602	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10404920	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10405064	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10405325	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10405407	0.90[EUR][1000 genomes]
rs10406177	0.85[EUR][1000 genomes]
rs10407084	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10409204	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10412043	0.89[EUR][1000 genomes]
rs10413602	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10414904	0.90[EUR][1000 genomes]
rs10415024	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10415358	0.92[EUR][1000 genomes]
rs10415937	0.90[EUR][1000 genomes]
rs10417503	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10417844	0.90[EUR][1000 genomes]
rs10420430	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10420722	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10420754	0.82[EUR][1000 genomes]
rs10422074	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10422423	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10422667	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10422967	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10424574	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10426297	0.83[EUR][1000 genomes]
rs10426618	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10426666	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10426699	0.92[EUR][1000 genomes]
rs12104380	0.87[EUR][1000 genomes]
rs12104381	0.89[EUR][1000 genomes]
rs12709812	0.85[EUR][1000 genomes]
rs12709813	0.90[EUR][1000 genomes]
rs12972252	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12979470	0.85[EUR][1000 genomes]
rs12981532	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12982333	0.82[EUR][1000 genomes]
rs13343471	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13343502	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13345116	0.90[EUR][1000 genomes]
rs13345148	0.90[EUR][1000 genomes]
rs1373991	0.90[EUR][1000 genomes]
rs1559229	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1823061	0.85[EUR][1000 genomes]
rs2081096	0.82[EUR][1000 genomes]
rs2112920	0.80[ASN][1000 genomes]
rs2112922	0.80[EUR][1000 genomes]
rs2112923	0.83[EUR][1000 genomes]
rs2303131	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28402338	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28538699	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28623164	0.85[EUR][1000 genomes]
rs2891699	0.85[EUR][1000 genomes]
rs35085437	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35777021	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3745765	0.92[EUR][1000 genomes]
rs3760825	0.83[EUR][1000 genomes]
rs3803895	0.90[EUR][1000 genomes]
rs4417644	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4452075	0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4801759	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4801803	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4802766	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4802889	0.80[ASN][1000 genomes]
rs4803229	0.94[EUR][1000 genomes]
rs4803347	0.90[EUR][1000 genomes]
rs4803460	0.90[EUR][1000 genomes]
rs4803539	0.90[EUR][1000 genomes]
rs4969487	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59224125	0.82[EUR][1000 genomes]
rs6508711	0.90[EUR][1000 genomes]
rs6508713	0.81[EUR][1000 genomes]
rs6508714	0.81[EUR][1000 genomes]
rs6508715	0.81[EUR][1000 genomes]
rs6508716	0.89[EUR][1000 genomes]
rs6508719	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs67293224	0.85[EUR][1000 genomes]
rs713256	0.86[AFR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7246993	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7247259	0.90[EUR][1000 genomes]
rs7252099	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7252325	0.85[EUR][1000 genomes]
rs7252346	0.85[EUR][1000 genomes]
rs7253091	0.82[EUR][1000 genomes]
rs7255407	0.85[EUR][1000 genomes]
rs7255972	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7256130	0.82[EUR][1000 genomes]
rs7257495	0.90[EUR][1000 genomes]
rs7257672	0.90[EUR][1000 genomes]
rs7258692	0.92[EUR][1000 genomes]
rs7259968	0.90[EUR][1000 genomes]
rs73631095	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7408133	0.92[EUR][1000 genomes]
rs7408446	0.80[EUR][1000 genomes]
rs7408563	0.92[EUR][1000 genomes]
rs8106839	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8109632	0.85[EUR][1000 genomes]
rs8111782	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8112610	0.82[EUR][1000 genomes]
rs9304566	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9676739	0.80[EUR][1000 genomes]
rs9676967	0.85[EUR][1000 genomes]
rs9917081	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv1058788	chr19:37857748-37899157	ZNF genes & repeats Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv579464	chr19:37858660-37881556	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv579465	chr19:37868552-37917692	ZNF genes & repeats Strong transcription Weak transcription Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37864000-37882000	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr19:37864000-37882000	ZNF genes & repeats	Liver	Liver
3	chr19:37864400-37880600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr19:37864400-37880800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
5	chr19:37864600-37880600	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
6	chr19:37864600-37890600	ZNF genes & repeats	Adipose Nuclei	Adipose
7	chr19:37865000-37875400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr19:37865000-37880600	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
9	chr19:37865200-37874600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr19:37865400-37880600	ZNF genes & repeats	Primary T cells from cord blood	blood
11	chr19:37865800-37875800	Strong transcription	Fetal Muscle Trunk	muscle
12	chr19:37867000-37878600	Weak transcription	Hela-S3	cervix
13	chr19:37868000-37880400	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
14	chr19:37868000-37880800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr19:37868000-37881000	ZNF genes & repeats	A549	lung
16	chr19:37868000-37882000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
17	chr19:37868000-37882200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
18	chr19:37868000-37886600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr19:37868200-37875200	Strong transcription	Brain Cingulate Gyrus	brain
20	chr19:37868200-37875200	Strong transcription	Brain Germinal Matrix	brain
21	chr19:37868200-37881000	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
22	chr19:37868200-37881600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
23	chr19:37868200-37882000	ZNF genes & repeats	Duodenum Mucosa	Duodenum
24	chr19:37868400-37880000	Strong transcription	Placenta Amnion	Placenta Amnion
25	chr19:37869400-37876000	Strong transcription	Skeletal Muscle Female	skeletal muscle
26	chr19:37869400-37881600	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
27	chr19:37869600-37877000	Strong transcription	Placenta	Placenta
28	chr19:37869600-37880800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr19:37869800-37874400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr19:37869800-37881600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
31	chr19:37870000-37875600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
32	chr19:37870000-37880600	ZNF genes & repeats	Ovary	ovary
33	chr19:37870000-37881600	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
34	chr19:37870000-37881800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr19:37870000-37882200	ZNF genes & repeats	Colon Smooth Muscle	Colon
36	chr19:37870600-37874400	ZNF genes & repeats	Fetal Lung	lung
37	chr19:37870600-37875200	Strong transcription	Right Ventricle	heart
38	chr19:37870600-37875200	Strong transcription	Osteobl	bone
39	chr19:37870600-37877200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr19:37870600-37877400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr19:37870800-37875400	ZNF genes & repeats	Fetal Intestine Large	intestine
42	chr19:37871000-37875600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr19:37871000-37880600	ZNF genes & repeats	Primary B cells from peripheral blood	blood
44	chr19:37871000-37881600	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
45	chr19:37871200-37882800	ZNF genes & repeats	Psoas Muscle	Psoas
46	chr19:37871400-37875000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr19:37871400-37875200	Strong transcription	Dnd41	blood
48	chr19:37871400-37875200	Weak transcription	NHEK	skin
49	chr19:37871400-37875800	Strong transcription	HSMM	muscle
50	chr19:37871600-37875000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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