Variant report

Variant	rs1783829
Chromosome Location	chr11:57419880-57419881
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:13)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:13 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:57419544-57420242	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr11:57411937-57420676	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr11:57410796-57421100	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr11:57410821-57420904	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr11:57417265-57420354	H1-hESC	embryonic stem cell:	n/a	n/a
6	JUND	chr11:57419825-57419952	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr11:57419538-57420303	ECC-1	luminal epithelium:	n/a	n/a
8	ELF1	chr11:57419722-57419983	K562	blood:	n/a	chr11:57419850-57419863
9	RUNX3	chr11:57419741-57420063	GM12878	blood:	n/a	n/a
10	SPI1	chr11:57419722-57420117	HL-60	blood:	n/a	n/a
11	POLR2A	chr11:57409804-57420281	PFSK-1	brain:	n/a	n/a
12	POLR2A	chr11:57419463-57420047	PFSK-1	brain:	n/a	n/a
13	RUNX3	chr11:57419736-57420061	GM12878	blood:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:57415751..57417478-chr11:57419075..57422993,4	K562	blood:
2	chr11:57419081..57422303-chr11:57422733..57426519,4	K562	blood:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZDHHC5-1	chr11:57417771-57420263	ENSG00000254602.1

No data

Variant related genes	Relation type
CLP1	TF binding region
YPEL4	TF binding region
ENSG00000254602	Chromatin interaction
ENSG00000166793	Chromatin interaction
ENSG00000172409	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1613592	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1624389	0.81[EUR][1000 genomes]
rs1631684	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1647394	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1647403	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1783818	0.80[EUR][1000 genomes]
rs1783827	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1783828	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1783980	0.81[EUR][1000 genomes]
rs1783983	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1783984	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1783985	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1785498	0.81[EUR][1000 genomes]
rs1798172	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1798173	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1798177	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7947357	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs929934	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[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	nsv1044030	chr11:57073395-58035564	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
2	nsv541047	chr11:57073395-58035564	Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv530621	chr11:57139699-57703639	Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
4	nsv832163	chr11:57299354-57481050	Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
5	nsv1040913	chr11:57315006-57696122	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
6	nsv832164	chr11:57407617-57578825	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
7	nsv508633	chr11:57419585-57560045	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1783829	TIMM10	Cis_1M	lymphoblastoid	RTeQTL
rs1783829	YPEL4	cis	lung	GTEx

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57417800-57420200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr11:57417800-57420200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr11:57417800-57424600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr11:57417800-57424600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr11:57418000-57420000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr11:57418000-57420000	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr11:57418000-57420000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr11:57418000-57420200	Weak transcription	Primary T cells from cord blood	blood
9	chr11:57418000-57420200	Weak transcription	NHLF	lung
10	chr11:57418000-57420400	Weak transcription	Fetal Lung	lung
11	chr11:57418000-57424200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr11:57418000-57424200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr11:57418000-57424200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr11:57418000-57424200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr11:57418000-57424400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr11:57418000-57424600	Weak transcription	Right Atrium	heart
17	chr11:57418000-57424600	Weak transcription	HSMM	muscle
18	chr11:57418200-57420000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr11:57418200-57420000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr11:57418200-57420200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr11:57418200-57420200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr11:57418200-57420200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr11:57418200-57420400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr11:57418200-57420600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr11:57418200-57424200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr11:57418200-57424200	Weak transcription	Brain Hippocampus Middle	brain
27	chr11:57418200-57424400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr11:57418400-57424600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr11:57418600-57420200	Weak transcription	K562	blood
30	chr11:57418600-57424200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr11:57418600-57424600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr11:57418800-57424600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr11:57419200-57420400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr11:57419600-57420200	Enhancers	Primary T cells fromperipheralblood	blood
35	chr11:57419600-57420200	Enhancers	Placenta	Placenta
36	chr11:57419600-57422600	Enhancers	Primary monocytes fromperipheralblood	blood
37	chr11:57419800-57420000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr11:57419800-57420000	Enhancers	Breast Myoepithelial Primary Cells	Breast
39	chr11:57419800-57420000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr11:57419800-57420000	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
41	chr11:57419800-57420200	Active TSS	Primary T helper cells fromperipheralblood	blood
42	chr11:57419800-57420200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr11:57419800-57420200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
44	chr11:57419800-57420200	Enhancers	Ovary	ovary
45	chr11:57419800-57420200	Active TSS	Monocytes-CD14+_RO01746	blood
46	chr11:57419800-57420400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
47	chr11:57419800-57421600	Enhancers	Primary hematopoietic stem cells short term culture	blood

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