Variant report

Variant	rs1923807
Chromosome Location	chr10:112583757-112583758
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	chr10:112583628-112583999	HepG2	liver:	n/a	chr10:112583806-112583817
2	CEBPB	chr10:112583663-112583949	K562	blood:	n/a	chr10:112583806-112583817
3	CEBPB	chr10:112583666-112584042	MCF-7	breast:	n/a	chr10:112583806-112583817
4	CEBPB	chr10:112583659-112583970	IMR90	lung:	n/a	chr10:112583806-112583817
5	CEBPB	chr10:112583676-112583994	H1-hESC	embryonic stem cell:	n/a	chr10:112583806-112583817
6	CEBPB	chr10:112583616-112584113	ECC-1	luminal epithelium:	n/a	chr10:112583806-112583817
7	CEBPB	chr10:112583647-112583976	A549	lung:	n/a	chr10:112583806-112583817
8	CEBPB	chr10:112583553-112584085	MCF-7	breast:	n/a	chr10:112583806-112583817

No.	Distal block	Cell Line	Cell type
1	chr10:112582540..112585422-chr10:112589787..112595688,6	MCF-7	breast:
2	chr10:112581444..112587243-chr10:112629842..112633404,6	MCF-7	breast:
3	chr10:112579505..112583802-chr10:112587400..112591373,5	MCF-7	breast:
4	chr10:112581723..112584048-chr10:112629413..112632345,2	K562	blood:
5	chr10:112580755..112589346-chr10:112627817..112636075,27	MCF-7	breast:
6	chr10:112582382..112584643-chr10:112585377..112589388,5	MCF-7	breast:

Variant related genes	Relation type
RBM20	TF binding region
ENSG00000203497	Chromatin interaction
ENSG00000203867	Chromatin interaction
ENSG00000150593	Chromatin interaction
ENSG00000232470	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10787283	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10885052	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10885053	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10885054	0.80[AMR][1000 genomes]
rs10885055	0.81[EUR][1000 genomes]
rs11195340	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1417634	0.81[EUR][1000 genomes]
rs1980689	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4918595	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4918598	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4918599	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4918600	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7072681	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs726803	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs726804	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs942076	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[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	nsv1045608	chr10:112524813-112677557	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv1041758	chr10:112552897-112677557	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv467455	chr10:112579299-112612471	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv552172	chr10:112579299-112612471	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv896003	chr10:112579299-112631211	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv896002	chr10:112579299-112638028	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	nsv1051566	chr10:112580049-112730573	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1923807	PDCD4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:112572600-112593800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr10:112576800-112584800	Enhancers	Psoas Muscle	Psoas
3	chr10:112577200-112590800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr10:112577400-112584800	Enhancers	Fetal Stomach	stomach
5	chr10:112577800-112593400	Weak transcription	Thymus	Thymus
6	chr10:112578000-112583800	Enhancers	Fetal Brain Male	brain
7	chr10:112578200-112584800	Enhancers	Placenta	Placenta
8	chr10:112578200-112585400	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr10:112578600-112584800	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr10:112578800-112587400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr10:112578800-112592400	Weak transcription	Primary T cells from cord blood	blood
12	chr10:112579400-112586000	Enhancers	Brain Germinal Matrix	brain
13	chr10:112580400-112583800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr10:112580400-112586800	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr10:112580400-112587400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr10:112580400-112587600	Weak transcription	Liver	Liver
17	chr10:112580400-112589800	Enhancers	Colon Smooth Muscle	Colon
18	chr10:112580600-112587000	Weak transcription	Lung	lung
19	chr10:112580800-112585000	Enhancers	Fetal Intestine Large	intestine
20	chr10:112581000-112585600	Enhancers	Pancreatic Islets	Pancreatic Islet
21	chr10:112581200-112584800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr10:112581200-112585000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr10:112581600-112584200	Enhancers	Fetal Thymus	thymus
24	chr10:112581600-112585200	Enhancers	Fetal Intestine Small	intestine
25	chr10:112582200-112584000	Enhancers	GM12878-XiMat	blood
26	chr10:112582200-112584200	Enhancers	Brain Hippocampus Middle	brain
27	chr10:112582400-112584000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr10:112582400-112584000	Enhancers	Primary B cells from peripheral blood	blood
29	chr10:112582400-112584600	Enhancers	HepG2	liver
30	chr10:112582600-112583800	Enhancers	Primary B cells from cord blood	blood
31	chr10:112582600-112585600	Enhancers	Rectal Mucosa Donor 31	rectum
32	chr10:112582600-112587000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr10:112582600-112593000	Weak transcription	K562	blood
34	chr10:112582600-112593400	Weak transcription	Gastric	stomach
35	chr10:112582800-112587400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr10:112583000-112584400	Enhancers	Stomach Smooth Muscle	stomach
37	chr10:112583000-112584600	Enhancers	Fetal Muscle Leg	muscle
38	chr10:112583000-112584600	Enhancers	Rectal Mucosa Donor 29	rectum
39	chr10:112583000-112585400	Strong transcription	Left Ventricle	heart
40	chr10:112583000-112585800	Enhancers	Skeletal Muscle Male	skeletal muscle
41	chr10:112583000-112586400	Weak transcription	Fetal Muscle Trunk	muscle
42	chr10:112583000-112587600	Weak transcription	Adipose Nuclei	Adipose
43	chr10:112583000-112587600	Weak transcription	Esophagus	oesophagus
44	chr10:112583000-112587600	Weak transcription	Ovary	ovary
45	chr10:112583000-112587600	Weak transcription	Right Ventricle	heart
46	chr10:112583200-112583800	Weak transcription	Aorta	Aorta
47	chr10:112583200-112584200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
48	chr10:112583200-112584400	Weak transcription	Brain Substantia Nigra	brain
49	chr10:112583200-112584400	Enhancers	Stomach Mucosa	stomach
50	chr10:112583200-112584800	Strong transcription	HSMMtube	muscle

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