Variant report

Variant	rs6510994
Chromosome Location	chr19:18750680-18750681
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr19:18750627-18750827	IMR90	lung:	n/a	n/a
2	CEBPB	chr19:18750614-18750844	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
KLHL26	TF binding region

Extended variants
information (count: 18 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs13344627	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1862646	0.91[ASN][1000 genomes]
rs28793742	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3795027	0.81[GIH][hapmap]
rs59186604	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs59333602	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73923135	1.00[ASN][1000 genomes]
rs754245	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8107586	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057795	chr19:18453362-18883844	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
2	nsv543925	chr19:18453362-18883844	Weak transcription Genic enhancers Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
3	nsv532615	chr19:18534867-18796031	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
4	nsv911281	chr19:18613917-18758255	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
5	nsv911282	chr19:18624964-18928480	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
6	nsv833776	chr19:18638028-18782264	Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
7	nsv911286	chr19:18652844-18811112	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
8	nsv911289	chr19:18700047-18811112	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
9	esv1849639	chr19:18747006-18780799	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6510994	MAST3	cis	cerebellum	SCAN
rs6510994	PGLS	cis	parietal	SCAN
rs6510994	MYO9B	cis	cerebellum	SCAN
rs6510994	GDF1	cis	parietal	SCAN
rs6510994	BRD4	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18748400-18761600	Weak transcription	Aorta	Aorta
2	chr19:18748600-18755800	Weak transcription	Ovary	ovary
3	chr19:18748600-18774400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr19:18748800-18751000	Weak transcription	Fetal Stomach	stomach
5	chr19:18748800-18754800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr19:18748800-18757400	Weak transcription	Fetal Kidney	kidney
7	chr19:18748800-18758600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr19:18748800-18759200	Weak transcription	Fetal Lung	lung
9	chr19:18749000-18751000	Weak transcription	Fetal Muscle Trunk	muscle
10	chr19:18749000-18751800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr19:18749000-18755200	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr19:18749000-18755400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr19:18749200-18750800	Enhancers	Colon Smooth Muscle	Colon
14	chr19:18749200-18754600	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr19:18749200-18754600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr19:18749200-18754800	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr19:18749200-18754800	Weak transcription	Brain Substantia Nigra	brain
18	chr19:18749200-18754800	Weak transcription	NHLF	lung
19	chr19:18749200-18754800	Weak transcription	Osteobl	bone
20	chr19:18749200-18755000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr19:18749200-18755000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr19:18749200-18755000	Weak transcription	Brain Cingulate Gyrus	brain
23	chr19:18749200-18755200	Weak transcription	Primary B cells from peripheral blood	blood
24	chr19:18749200-18756200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr19:18749200-18757200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr19:18749200-18757400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr19:18749200-18757600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr19:18749200-18759000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr19:18749200-18759600	Weak transcription	Thymus	Thymus
30	chr19:18749200-18759800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr19:18749200-18768200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr19:18749200-18778400	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr19:18749400-18751000	Weak transcription	Stomach Mucosa	stomach
34	chr19:18749400-18752600	Weak transcription	Hela-S3	cervix
35	chr19:18749400-18754800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr19:18749400-18754800	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr19:18749400-18754800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr19:18749400-18754800	Weak transcription	Brain Anterior Caudate	brain
39	chr19:18749400-18754800	Weak transcription	GM12878-XiMat	blood
40	chr19:18749400-18754800	Weak transcription	Monocytes-CD14+_RO01746	blood
41	chr19:18749400-18755000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr19:18749400-18755000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr19:18749400-18755000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr19:18749400-18755000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr19:18749400-18755000	Weak transcription	Right Atrium	heart
46	chr19:18749400-18755000	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr19:18749400-18755200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr19:18749400-18755200	Weak transcription	Adipose Nuclei	Adipose
49	chr19:18749400-18755200	Weak transcription	Esophagus	oesophagus
50	chr19:18749400-18755200	Weak transcription	Lung	lung

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