Variant report

Variant	rs1501195
Chromosome Location	chr3:134899276-134899277
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	chr20:45983957..45986811-chr3:134898181..134900644,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000101040	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1021753	0.95[ASN][1000 genomes]
rs1021754	0.95[ASN][1000 genomes]
rs1027608	0.80[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16842755	0.83[CHD][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs1875371	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs28594191	0.83[AMR][1000 genomes]
rs35779003	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3772636	0.83[CEU][hapmap];0.92[EUR][1000 genomes]
rs3772638	0.83[MEX][hapmap]
rs3821502	0.88[CEU][hapmap];0.87[GIH][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs4441681	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4569682	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4894257	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4894258	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4894280	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4894286	0.94[ASW][hapmap];0.96[CEU][hapmap];0.84[CHB][hapmap];0.84[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.80[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4894287	0.87[ASW][hapmap];0.87[CEU][hapmap];0.84[CHB][hapmap];0.82[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4894289	0.92[EUR][1000 genomes]
rs4894290	0.92[EUR][1000 genomes]
rs6763009	0.88[CEU][hapmap];0.87[GIH][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs6776570	0.92[CEU][hapmap];0.87[GIH][hapmap];0.92[TSI][hapmap];0.92[EUR][1000 genomes]
rs6799448	0.96[CEU][hapmap];0.94[JPT][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6799471	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs875368	0.88[JPT][hapmap];0.92[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs875369	0.92[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs875370	0.84[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs882059	0.84[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs882060	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9822213	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9837009	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[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	nsv1000277	chr3:134546080-134970837	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv877516	chr3:134689420-134918522	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1501195	CEP63	cis	parietal	SCAN
rs1501195	TXNDC6	cis	cerebellum	SCAN
rs1501195	PPP2R3A	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:134874800-134901800	Weak transcription	GM12878-XiMat	blood
2	chr3:134885000-134904400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
3	chr3:134885600-134911800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr3:134885600-134912200	Weak transcription	Brain Germinal Matrix	brain
5	chr3:134887600-134911400	Weak transcription	Brain Hippocampus Middle	brain
6	chr3:134888200-134900000	Weak transcription	Fetal Brain Female	brain
7	chr3:134888200-134908600	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr3:134889000-134910200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr3:134889000-134924600	Weak transcription	Brain Anterior Caudate	brain
10	chr3:134890600-134899400	Weak transcription	Fetal Brain Male	brain
11	chr3:134890800-134906800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr3:134893200-134900000	Weak transcription	Brain Cingulate Gyrus	brain
13	chr3:134895800-134912000	Weak transcription	Brain Angular Gyrus	brain

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