Variant report

Variant	rs2967428
Chromosome Location	chr19:37105315-37105316
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10408063	0.87[AFR][1000 genomes]
rs10408318	0.90[AFR][1000 genomes]
rs10411150	0.88[AFR][1000 genomes]
rs10413697	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10414240	0.87[AFR][1000 genomes]
rs10417106	0.90[AFR][1000 genomes]
rs10417344	0.91[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10418271	0.87[AFR][1000 genomes]
rs10422700	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10425382	0.90[AFR][1000 genomes]
rs1227798	1.00[MEX][hapmap];0.83[YRI][hapmap]
rs1227813	0.82[ASW][hapmap];0.85[LWK][hapmap];0.83[YRI][hapmap]
rs1234513	0.88[AFR][1000 genomes]
rs12459915	0.85[AFR][1000 genomes]
rs12462268	0.87[AFR][1000 genomes]
rs13345382	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17468285	0.82[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes]
rs28418630	0.80[AFR][1000 genomes]
rs28465595	0.87[AFR][1000 genomes]
rs28472526	0.87[AFR][1000 genomes]
rs28645577	0.81[AFR][1000 genomes]
rs28742010	0.81[AFR][1000 genomes]
rs28818888	0.87[AFR][1000 genomes]
rs2912407	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2912409	0.91[YRI][hapmap];1.00[AMR][1000 genomes]
rs2912413	1.00[MEX][hapmap]
rs2912418	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2945986	1.00[MEX][hapmap];0.92[YRI][hapmap];1.00[AMR][1000 genomes]
rs2967425	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2967426	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2967430	0.91[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2967538	1.00[AMR][1000 genomes]
rs35621405	0.87[AFR][1000 genomes]
rs58880289	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59951429	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60268308	0.85[AFR][1000 genomes]
rs60615280	0.84[AFR][1000 genomes]
rs6510562	0.87[AFR][1000 genomes]
rs7251193	0.82[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[YRI][hapmap]
rs7252295	1.00[MEX][hapmap]
rs73607078	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73609133	0.87[AFR][1000 genomes]
rs73609981	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73612010	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73612013	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73612039	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73612043	0.87[AFR][1000 genomes]
rs73612047	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73612050	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73612052	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73615692	0.87[AFR][1000 genomes]
rs73617803	0.83[AFR][1000 genomes]
rs8104355	0.82[AFR][1000 genomes]
rs8111419	0.87[AFR][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	nsv1064851	chr19:36910259-37689721	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Active TSS 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 miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv1065698	chr19:36916796-37690124	Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv543999	chr19:36916796-37690124	Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers 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	61 gene(s)	inside rSNPs	diseases
4	nsv529817	chr19:36930549-37654062	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
5	nsv833817	chr19:36978852-37195695	ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
6	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
7	esv3434386	chr19:37073454-37114509	Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2967428	DNAJC5B	trans	lymphoblastoid	seeQTL

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37096800-37110000	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr19:37097000-37106000	Weak transcription	Fetal Thymus	thymus
3	chr19:37097000-37106800	Weak transcription	Stomach Mucosa	stomach
4	chr19:37097000-37107000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr19:37097000-37107000	Weak transcription	Small Intestine	intestine
6	chr19:37097000-37107400	Weak transcription	HUVEC	blood vessel
7	chr19:37097000-37107800	Weak transcription	Gastric	stomach
8	chr19:37097000-37112600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr19:37097200-37105600	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr19:37097200-37109600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr19:37097200-37110000	Weak transcription	NHLF	lung
12	chr19:37098000-37106200	Strong transcription	Brain Hippocampus Middle	brain
13	chr19:37098000-37118200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr19:37098000-37156000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr19:37098200-37108400	Strong transcription	Brain Inferior Temporal Lobe	brain
16	chr19:37098200-37120400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr19:37098400-37107400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr19:37098600-37105600	Strong transcription	Brain Angular Gyrus	brain
19	chr19:37098600-37106200	Strong transcription	Ovary	ovary
20	chr19:37098800-37106000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr19:37098800-37108200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr19:37099000-37105600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr19:37099000-37109200	Strong transcription	Dnd41	blood
24	chr19:37099200-37105800	Strong transcription	Stomach Smooth Muscle	stomach
25	chr19:37099200-37110000	Strong transcription	Brain Cingulate Gyrus	brain
26	chr19:37099600-37105800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr19:37099600-37108400	Strong transcription	Fetal Muscle Leg	muscle
28	chr19:37100200-37107600	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr19:37101000-37107000	Weak transcription	Aorta	Aorta
30	chr19:37101000-37107000	Weak transcription	Pancreas	Pancrea
31	chr19:37101000-37107000	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr19:37101400-37112800	Weak transcription	Osteobl	bone
33	chr19:37101800-37111000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr19:37102000-37105600	Weak transcription	Left Ventricle	heart
35	chr19:37102000-37105600	Weak transcription	Psoas Muscle	Psoas
36	chr19:37102000-37106800	Weak transcription	HSMMtube	muscle
37	chr19:37102000-37118600	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
38	chr19:37102200-37135200	ZNF genes & repeats	Fetal Brain Female	brain
39	chr19:37102800-37107000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr19:37103000-37106000	ZNF genes & repeats	Primary T cells from cord blood	blood
41	chr19:37103000-37118600	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
42	chr19:37103200-37106400	Weak transcription	Fetal Kidney	kidney
43	chr19:37103200-37108200	Weak transcription	Brain Substantia Nigra	brain
44	chr19:37103200-37109200	Weak transcription	Right Ventricle	heart
45	chr19:37103400-37105600	Strong transcription	Primary B cells from cord blood	blood
46	chr19:37103400-37106200	Weak transcription	Fetal Heart	heart
47	chr19:37103400-37106800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr19:37103400-37107000	Weak transcription	Colon Smooth Muscle	Colon
49	chr19:37103600-37105400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr19:37103600-37105600	Strong transcription	NHDF-Ad	bronchial

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