Variant report

Variant	rs12601350
Chromosome Location	chr17:46120419-46120420
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:46117511..46121845-chr17:46183690..46186313,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000002919	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs12051	0.94[ASN][1000 genomes]
rs12600980	0.86[EUR][1000 genomes]
rs12602131	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12602670	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12946143	0.89[EUR][1000 genomes]
rs1473117	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16951519	0.93[EUR][1000 genomes]
rs2023885	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2229369	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2240119	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2240120	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2240121	0.89[EUR][1000 genomes]
rs2285860	0.85[EUR][1000 genomes]
rs2325783	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3785737	0.83[EUR][1000 genomes]
rs4995899	0.93[EUR][1000 genomes]
rs55920502	0.93[EUR][1000 genomes]
rs55982711	0.85[EUR][1000 genomes]
rs58554000	0.87[AFR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72823519	0.85[EUR][1000 genomes]
rs72823528	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72823532	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72823533	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs757353	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8066049	0.82[EUR][1000 genomes]
rs8071199	0.83[EUR][1000 genomes]
rs978263	0.86[EUR][1000 genomes]
rs9890691	0.83[EUR][1000 genomes]
rs9898218	0.94[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
rs12601350	CBX1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46115600-46123800	Weak transcription	Brain Substantia Nigra	brain
2	chr17:46115800-46120600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr17:46115800-46122600	Weak transcription	Esophagus	oesophagus
4	chr17:46115800-46122800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr17:46115800-46122800	Weak transcription	Brain Anterior Caudate	brain
6	chr17:46115800-46122800	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr17:46115800-46123200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr17:46115800-46123200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr17:46116000-46122600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr17:46116000-46122600	Weak transcription	NH-A	brain
11	chr17:46116000-46123000	Weak transcription	NHLF	lung
12	chr17:46116000-46124000	Weak transcription	Brain Hippocampus Middle	brain
13	chr17:46117000-46122600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr17:46119200-46121400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr17:46119400-46123400	Weak transcription	A549	lung
16	chr17:46119400-46123800	Weak transcription	Primary hematopoietic stem cells	blood
17	chr17:46120200-46121400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr17:46120200-46121400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr17:46120200-46121400	Enhancers	NHEK	skin
20	chr17:46120200-46121600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr17:46120200-46121800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr17:46120200-46122600	Enhancers	Skeletal Muscle Female	skeletal muscle
23	chr17:46120200-46122800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr17:46120200-46123000	Enhancers	NHDF-Ad	bronchial
25	chr17:46120400-46120600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr17:46120400-46120600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr17:46120400-46120600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
28	chr17:46120400-46120600	Enhancers	Placenta	Placenta
29	chr17:46120400-46120800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr17:46120400-46120800	Enhancers	Psoas Muscle	Psoas
31	chr17:46120400-46121200	Enhancers	Muscle Satellite Cultured Cells	--
32	chr17:46120400-46121200	Enhancers	HMEC	breast
33	chr17:46120400-46121200	Enhancers	K562	blood
34	chr17:46120400-46121400	Enhancers	HSMMtube	muscle
35	chr17:46120400-46121400	Enhancers	Osteobl	bone
36	chr17:46120400-46121600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr17:46120400-46121600	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr17:46120400-46122600	Enhancers	HSMM	muscle

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