Variant report

Variant	rs11545619
Chromosome Location	chr19:53116643-53116644
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:52406735..52408758-chr19:53114766..53117318,2	K562	blood:
2	chr19:53115970..53118193-chr19:53236786..53238588,2	K562	blood:
3	chr19:53109944..53111454-chr19:53116244..53117812,2	K562	blood:
4	chr19:53115087..53117490-chr19:53126115..53129040,2	K562	blood:

Variant related genes	Relation type
ENSG00000198093	Chromatin interaction
ENSG00000213020	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs12610407	0.83[ASN][1000 genomes]
rs12974834	1.00[CEU][hapmap]
rs12976870	1.00[CEU][hapmap]
rs12978061	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13103	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17633389	1.00[JPT][hapmap]
rs34813370	0.84[EUR][1000 genomes]
rs6509661	1.00[CEU][hapmap]
rs66599469	0.90[EUR][1000 genomes]
rs71358890	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8108275	1.00[CEU][hapmap];0.83[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv1065584	chr19:53043126-53127459	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv833874	chr19:53058014-53257875	Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv912305	chr19:53092465-53349850	Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	nsv912306	chr19:53092465-53400760	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	nsv912307	chr19:53092465-53433054	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
7	nsv912308	chr19:53092465-53436337	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
8	nsv912309	chr19:53092465-53440653	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
9	nsv912310	chr19:53092465-53451291	Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Enhancers Genic enhancers 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	33 gene(s)	inside rSNPs	diseases
10	nsv828616	chr19:53095216-53137823	Weak transcription ZNF genes & repeats Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
11	nsv912311	chr19:53103875-53212361	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
12	nsv912312	chr19:53103875-53296371	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
13	nsv912313	chr19:53103875-53436337	ZNF genes & repeats Weak transcription Strong transcription Active TSS 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	30 gene(s)	inside rSNPs	diseases
14	nsv912314	chr19:53105547-53144082	Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	9 gene(s)	inside rSNPs	diseases
15	nsv912315	chr19:53105547-53149967	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	9 gene(s)	inside rSNPs	diseases
16	nsv912316	chr19:53105547-53158023	Flanking Active TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
17	nsv912317	chr19:53105547-53440653	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
18	nsv1066762	chr19:53112568-53552217	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
19	nsv527815	chr19:53114267-53117531	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
20	nsv817857	chr19:53114267-53120559	ZNF genes & repeats Weak transcription Strong transcription	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11545619	ZNF83	cis	lymphoblastoid	seeQTL
rs11545619	ZNF83	cis	Whole Blood	GTEx
rs11545619	ZNF83	Cis_1M	lymphoblastoid	RTeQTL
rs11545619	ZNF83	cis	multi-tissue	Pritchard

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:53105200-53120200	Weak transcription	Aorta	Aorta
2	chr19:53105400-53121200	Weak transcription	Fetal Brain Male	brain
3	chr19:53105800-53117000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr19:53105800-53129000	Weak transcription	Hela-S3	cervix
5	chr19:53107000-53136600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr19:53110600-53119400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr19:53112000-53117400	ZNF genes & repeats	Fetal Intestine Large	intestine
8	chr19:53112000-53131600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
9	chr19:53112400-53123400	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr19:53112800-53123200	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr19:53113000-53120000	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr19:53113200-53119400	ZNF genes & repeats	Duodenum Mucosa	Duodenum
13	chr19:53113200-53121600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr19:53113400-53119800	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
15	chr19:53113400-53122000	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
16	chr19:53113800-53123800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr19:53114200-53122200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr19:53114800-53117400	Strong transcription	Cortex derived primary cultured neurospheres	brain
19	chr19:53114800-53121600	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr19:53115000-53117800	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr19:53115000-53118000	ZNF genes & repeats	Muscle Satellite Cultured Cells	--
22	chr19:53115000-53121000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr19:53115000-53122000	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr19:53115200-53120600	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
25	chr19:53115200-53120800	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
26	chr19:53115200-53121200	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr19:53115200-53121600	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
28	chr19:53115200-53122000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
29	chr19:53115400-53117800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr19:53115400-53119000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
31	chr19:53115400-53119800	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr19:53115400-53120000	Strong transcription	Fetal Lung	lung
33	chr19:53115400-53120200	Strong transcription	Rectal Smooth Muscle	rectum
34	chr19:53115400-53120400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr19:53115400-53120600	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr19:53115400-53120800	ZNF genes & repeats	Primary B cells from cord blood	blood
37	chr19:53115400-53120800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr19:53115400-53120800	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
39	chr19:53115400-53121400	ZNF genes & repeats	Primary B cells from peripheral blood	blood
40	chr19:53115400-53121400	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
41	chr19:53115400-53121600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr19:53115400-53121600	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
43	chr19:53115400-53121600	Strong transcription	Brain Germinal Matrix	brain
44	chr19:53115400-53122600	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
45	chr19:53115400-53123800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr19:53115400-53123800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
47	chr19:53115400-53131800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr19:53115600-53117000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr19:53115600-53117000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr19:53115600-53117000	Weak transcription	Pancreas	Pancrea

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