Variant report

Variant	rs2682561
Chromosome Location	chr19:44041425-44041426
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs12981701	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12983281	0.91[ASN][1000 genomes]
rs1475933	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2022062	0.89[EUR][1000 genomes]
rs2030404	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2139720	0.89[ASN][1000 genomes]
rs25479	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs25485	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2599461	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2599462	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2682563	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2854500	0.86[ASN][1000 genomes]
rs2854501	0.86[ASN][1000 genomes]
rs3213276	0.82[EUR][1000 genomes]
rs3213329	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3213333	0.86[ASN][1000 genomes]
rs3213334	0.86[ASN][1000 genomes]
rs3213356	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3213387	0.91[ASN][1000 genomes]
rs3547	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56012842	0.93[ASN][1000 genomes]
rs73043690	0.91[ASN][1000 genomes]
rs762507	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs915927	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1055872	chr19:43173614-44075193	Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv544009	chr19:43173614-44075193	Enhancers ZNF genes & repeats Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv1067126	chr19:43260649-44075194	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	nsv544015	chr19:43260649-44075194	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
5	nsv1057657	chr19:43302497-44076564	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
6	nsv1059631	chr19:43316978-44075054	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
7	nsv544030	chr19:43316978-44075054	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
8	nsv532820	chr19:43807486-44080610	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
9	nsv1056721	chr19:43808474-44095077	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
10	nsv532821	chr19:43842383-44357315	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
11	nsv1058162	chr19:43846238-44055058	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
12	nsv1056785	chr19:44010370-44081601	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
13	nsv912107	chr19:44030998-44055726	Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2682561	ZNF575	cis	Artery Tibial	GTEx
rs2682561	ETHE1	Cis_1M	lymphoblastoid	RTeQTL
rs2682561	ZNF575	cis	lung	GTEx
rs2682561	ZNF575	cis	Adipose Subcutaneous	GTEx
rs2682561	ZNF575	cis	Nerve Tibial	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44038000-44042400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr19:44038000-44046800	Weak transcription	Small Intestine	intestine
3	chr19:44038200-44042400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr19:44038200-44042600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr19:44038200-44042600	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr19:44038200-44042600	Weak transcription	HepG2	liver
7	chr19:44038200-44042600	Weak transcription	HSMMtube	muscle
8	chr19:44038400-44041800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr19:44038400-44042600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr19:44038400-44043000	Weak transcription	GM12878-XiMat	blood
11	chr19:44038400-44043200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr19:44038400-44043400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr19:44038600-44041800	Weak transcription	Ovary	ovary
14	chr19:44038600-44042000	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr19:44038600-44042200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr19:44038600-44042400	Weak transcription	Left Ventricle	heart
17	chr19:44038600-44042600	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr19:44038600-44042600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr19:44038600-44042600	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr19:44038600-44043400	Weak transcription	NHEK	skin
21	chr19:44038600-44054000	Weak transcription	Psoas Muscle	Psoas
22	chr19:44038800-44041600	Weak transcription	Primary monocytes fromperipheralblood	blood
23	chr19:44038800-44041600	Weak transcription	Fetal Intestine Large	intestine
24	chr19:44038800-44042400	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr19:44038800-44042400	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr19:44038800-44042400	Weak transcription	Duodenum Mucosa	Duodenum
27	chr19:44038800-44042400	Weak transcription	HSMM	muscle
28	chr19:44038800-44042400	Weak transcription	Monocytes-CD14+_RO01746	blood
29	chr19:44038800-44042600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr19:44038800-44042600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr19:44038800-44042600	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr19:44038800-44042600	Weak transcription	Fetal Kidney	kidney
33	chr19:44038800-44042600	Weak transcription	K562	blood
34	chr19:44038800-44042800	Weak transcription	Primary B cells from cord blood	blood
35	chr19:44038800-44044400	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr19:44038800-44046800	Weak transcription	Esophagus	oesophagus
37	chr19:44038800-44055800	Weak transcription	Stomach Mucosa	stomach
38	chr19:44039000-44041600	Weak transcription	Adipose Nuclei	Adipose
39	chr19:44039000-44041600	Weak transcription	Fetal Thymus	thymus
40	chr19:44039000-44041800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr19:44039000-44041800	Weak transcription	Primary hematopoietic stem cells	blood
42	chr19:44039000-44042200	Weak transcription	A549	lung
43	chr19:44039000-44042400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr19:44039000-44042400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr19:44039000-44042400	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr19:44039000-44042600	Weak transcription	Primary B cells from peripheral blood	blood
47	chr19:44039000-44042600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr19:44039000-44042600	Weak transcription	NHDF-Ad	bronchial
49	chr19:44039000-44042800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr19:44039000-44044600	Weak transcription	NHLF	lung

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