Variant report

Variant	rs1473117
Chromosome Location	chr17:46092539-46092540
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:46091408..46093930-chr17:46096491..46098890,2	MCF-7	breast:
2	chr17:46058200..46059806-chr17:46090614..46093225,2	MCF-7	breast:
3	chr17:45973797..45976110-chr17:46092219..46094181,2	MCF-7	breast:
4	chr17:46042235..46044126-chr17:46090847..46093838,2	K562	blood:

Variant related genes	Relation type
ENSG00000108465	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs12051	0.93[ASN][1000 genomes]
rs12601350	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12602131	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12602670	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16951519	0.83[EUR][1000 genomes]
rs17616799	0.86[EUR][1000 genomes]
rs2023885	0.85[EUR][1000 genomes]
rs2229369	0.85[EUR][1000 genomes]
rs2240119	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2240120	0.85[EUR][1000 genomes]
rs2285860	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2325783	0.85[EUR][1000 genomes]
rs2525105	0.83[EUR][1000 genomes]
rs4995899	0.83[EUR][1000 genomes]
rs55920502	0.83[EUR][1000 genomes]
rs55982711	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56402159	0.86[EUR][1000 genomes]
rs57782323	0.90[EUR][1000 genomes]
rs58554000	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61396871	0.86[EUR][1000 genomes]
rs72823519	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72823528	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72823532	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72823533	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs757353	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9898218	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469808	chr17:46049868-46228673	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
2	nsv482897	chr17:46049868-46228673	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1473117	CBX1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46089400-46095000	Weak transcription	A549	lung
2	chr17:46089600-46092800	Enhancers	Fetal Brain Male	brain
3	chr17:46089800-46092800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr17:46089800-46094000	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr17:46090000-46092600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr17:46090000-46093400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr17:46090000-46093600	Weak transcription	HSMM	muscle
8	chr17:46090000-46095800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr17:46090200-46092800	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
10	chr17:46090200-46092800	Enhancers	Brain Germinal Matrix	brain
11	chr17:46090200-46093600	Weak transcription	Spleen	Spleen
12	chr17:46090200-46093800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr17:46090200-46100400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr17:46090200-46100400	Weak transcription	Brain Substantia Nigra	brain
15	chr17:46090400-46092800	Enhancers	Fetal Brain Female	brain
16	chr17:46090400-46093400	Weak transcription	HSMMtube	muscle
17	chr17:46090400-46100800	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr17:46091200-46092600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
19	chr17:46091200-46092800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr17:46091400-46092600	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
21	chr17:46091400-46092800	Bivalent Enhancer	Fetal Muscle Leg	muscle
22	chr17:46091400-46095000	Weak transcription	Fetal Thymus	thymus
23	chr17:46091400-46095800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr17:46091600-46092600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr17:46091600-46092800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr17:46091600-46093000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
27	chr17:46091600-46093000	Enhancers	Placenta	Placenta
28	chr17:46091600-46093000	Enhancers	K562	blood
29	chr17:46091600-46093200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
30	chr17:46091600-46094000	Enhancers	Fetal Stomach	stomach
31	chr17:46091800-46092600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr17:46091800-46092600	Enhancers	Placenta Amnion	Placenta Amnion
33	chr17:46091800-46092800	Enhancers	HUES64 Cell Line	embryonic stem cell
34	chr17:46092000-46092600	Enhancers	Brain Anterior Caudate	brain
35	chr17:46092000-46093000	Enhancers	H1 Cell Line	embryonic stem cell
36	chr17:46092200-46092600	Enhancers	HUES6 Cell Line	embryonic stem cell
37	chr17:46092200-46092800	Enhancers	iPS-18 Cell Line	embryonic stem cell
38	chr17:46092200-46095200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr17:46092400-46092600	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell

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