Variant report

Variant	rs2133307
Chromosome Location	chr3:134065640-134065641
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:134024378..134037377-chr3:134063304..134080412,83	MCF-7	breast:

Variant related genes	Relation type
ENSG00000240006	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1111516	0.96[CEU][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11708815	0.90[ASN][1000 genomes]
rs11719057	0.90[ASN][1000 genomes]
rs13075185	0.90[ASN][1000 genomes]
rs1353776	0.96[CEU][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1466827	0.86[ASN][1000 genomes]
rs1498731	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1603824	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2400278	0.96[CEU][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2400279	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2400280	0.93[ASN][1000 genomes]
rs34341902	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35951257	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3732852	0.96[CEU][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3773820	0.90[ASN][1000 genomes]
rs3821705	0.96[CEU][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4264700	0.95[ASN][1000 genomes]
rs4974485	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4974487	0.84[ASN][1000 genomes]
rs4974489	0.95[ASN][1000 genomes]
rs4974491	0.95[ASN][1000 genomes]
rs4974494	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4974495	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4974496	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4974497	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4974498	0.96[CEU][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6439477	0.96[CEU][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6439478	0.83[CEU][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6786148	0.95[ASN][1000 genomes]
rs7613066	0.90[ASN][1000 genomes]
rs7643419	0.94[YRI][hapmap]
rs9450	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9817900	0.95[ASN][1000 genomes]
rs9853621	0.95[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	esv3522171	chr3:133889405-134156571	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	esv3522172	chr3:133889405-134156571	Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs2133307	RP11-375I20.6	cis	Thyroid	GTEx
rs2133307	RP11-375I20.6	cis	Skin Sun Exposed Lower leg	GTEx
rs2133307	RP11-375I20.6	cis	Artery Tibial	GTEx
rs2133307	RP11-375I20.6	cis	Adipose Subcutaneous	GTEx
rs2133307	RP11-375I20.6	cis	Artery Aorta	GTEx
rs2133307	RP11-375I20.6	cis	Esophagus Muscularis	GTEx
rs2133307	RP11-375I20.6	cis	lung	GTEx
rs2133307	RP11-375I20.6	cis	Nerve Tibial	GTEx
rs2133307	RP11-375I20.6	cis	Heart Left Ventricle	GTEx

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:134054200-134069800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:134054400-134069400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr3:134055800-134071000	Weak transcription	Rectal Smooth Muscle	rectum
4	chr3:134056200-134066600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr3:134057200-134067400	Weak transcription	Fetal Heart	heart
6	chr3:134058600-134069200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr3:134060600-134067200	Weak transcription	Lung	lung
8	chr3:134060600-134067800	Weak transcription	Stomach Smooth Muscle	stomach
9	chr3:134060600-134070000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr3:134060800-134067200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr3:134060800-134072200	Weak transcription	Fetal Kidney	kidney
12	chr3:134061200-134068400	Weak transcription	Fetal Stomach	stomach
13	chr3:134061200-134069000	Weak transcription	Fetal Brain Female	brain
14	chr3:134061400-134073000	Weak transcription	Fetal Brain Male	brain
15	chr3:134063600-134066600	Weak transcription	Psoas Muscle	Psoas
16	chr3:134065000-134065800	ZNF genes & repeats	Adipose Nuclei	Adipose
17	chr3:134065000-134065800	ZNF genes & repeats	HSMM	muscle
18	chr3:134065000-134066000	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr3:134065000-134066200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr3:134065000-134066600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
21	chr3:134065200-134065800	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
22	chr3:134065200-134065800	ZNF genes & repeats	Spleen	Spleen
23	chr3:134065200-134066000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
24	chr3:134065200-134066200	ZNF genes & repeats	A549	lung
25	chr3:134065400-134065800	ZNF genes & repeats	Liver	Liver
26	chr3:134065400-134066400	Weak transcription	Pancreas	Pancrea
27	chr3:134065600-134065800	ZNF genes & repeats	Brain Hippocampus Middle	brain
28	chr3:134065600-134065800	ZNF genes & repeats	Left Ventricle	heart
29	chr3:134065600-134066400	Weak transcription	Gastric	stomach
30	chr3:134065600-134067200	Weak transcription	Right Ventricle	heart
31	chr3:134065600-134067400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr3:134065600-134067600	Weak transcription	Brain Germinal Matrix	brain

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