Variant report

Variant	rs4918600
Chromosome Location	chr10:112584451-112584452
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	USF1	chr10:112584396-112584814	ECC-1	luminal epithelium:	n/a	chr10:112584584-112584595 chr10:112584644-112584655
2	USF1	chr10:112584416-112584789	ECC-1	luminal epithelium:	n/a	chr10:112584584-112584595 chr10:112584644-112584655
3	USF1	chr10:112584424-112584779	K562	blood:	n/a	chr10:112584584-112584595 chr10:112584644-112584655
4	POLR2A	chr10:112584146-112584677	K562	blood:	n/a	n/a

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	chr10:112580755..112589346-chr10:112627817..112636075,27	MCF-7	breast:
4	chr10:112582382..112584643-chr10:112585377..112589388,5	MCF-7	breast:

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

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10736209	0.86[AMR][1000 genomes]
rs10787283	0.96[CEU][hapmap];0.91[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10885052	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10885053	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10885054	0.85[CEU][hapmap];0.84[CHB][hapmap];0.85[JPT][hapmap];0.84[AMR][1000 genomes]
rs10885055	0.89[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11195340	0.81[EUR][1000 genomes]
rs12573386	0.85[JPT][hapmap]
rs1923807	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1980689	0.88[CEU][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2031128	0.85[JPT][hapmap]
rs4918595	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4918598	0.92[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4918599	0.96[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4918601	0.84[CEU][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs7072681	0.92[CEU][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs726803	0.87[CEU][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs726804	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7922732	0.87[CEU][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes]
rs942076	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[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
rs4918600	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	chr10:112578200-112584800	Enhancers	Placenta	Placenta
7	chr10:112578200-112585400	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr10:112578600-112584800	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr10:112578800-112587400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr10:112578800-112592400	Weak transcription	Primary T cells from cord blood	blood
11	chr10:112579400-112586000	Enhancers	Brain Germinal Matrix	brain
12	chr10:112580400-112586800	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr10:112580400-112587400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr10:112580400-112587600	Weak transcription	Liver	Liver
15	chr10:112580400-112589800	Enhancers	Colon Smooth Muscle	Colon
16	chr10:112580600-112587000	Weak transcription	Lung	lung
17	chr10:112580800-112585000	Enhancers	Fetal Intestine Large	intestine
18	chr10:112581000-112585600	Enhancers	Pancreatic Islets	Pancreatic Islet
19	chr10:112581200-112584800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr10:112581200-112585000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr10:112581600-112585200	Enhancers	Fetal Intestine Small	intestine
22	chr10:112582400-112584600	Enhancers	HepG2	liver
23	chr10:112582600-112585600	Enhancers	Rectal Mucosa Donor 31	rectum
24	chr10:112582600-112587000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr10:112582600-112593000	Weak transcription	K562	blood
26	chr10:112582600-112593400	Weak transcription	Gastric	stomach
27	chr10:112582800-112587400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr10:112583000-112584600	Enhancers	Fetal Muscle Leg	muscle
29	chr10:112583000-112584600	Enhancers	Rectal Mucosa Donor 29	rectum
30	chr10:112583000-112585400	Strong transcription	Left Ventricle	heart
31	chr10:112583000-112585800	Enhancers	Skeletal Muscle Male	skeletal muscle
32	chr10:112583000-112586400	Weak transcription	Fetal Muscle Trunk	muscle
33	chr10:112583000-112587600	Weak transcription	Adipose Nuclei	Adipose
34	chr10:112583000-112587600	Weak transcription	Esophagus	oesophagus
35	chr10:112583000-112587600	Weak transcription	Ovary	ovary
36	chr10:112583000-112587600	Weak transcription	Right Ventricle	heart
37	chr10:112583200-112584800	Strong transcription	HSMMtube	muscle
38	chr10:112583200-112585600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr10:112583200-112585600	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr10:112583200-112585600	Genic enhancers	Fetal Heart	heart
41	chr10:112583200-112587400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr10:112583200-112587600	Weak transcription	Pancreas	Pancrea
43	chr10:112583200-112587800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr10:112583200-112588000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr10:112583200-112588200	Weak transcription	Colonic Mucosa	Colon
46	chr10:112583200-112593400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr10:112583400-112584600	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr10:112583400-112584800	Enhancers	Skeletal Muscle Female	skeletal muscle
49	chr10:112583400-112585800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr10:112583400-112587400	Weak transcription	Fetal Lung	lung

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