Variant report

Variant	rs6776570
Chromosome Location	chr3:134911917-134911918
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	chr3:134904377..134907908-chr3:134908448..134912165,3	MCF-7	breast:
2	chr3:134908383..134910527-chr3:134911083..134913676,4	MCF-7	breast:

Extended variants
information (count: 28 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs1027608	0.90[EUR][1000 genomes]
rs1501195	0.92[CEU][hapmap];0.87[GIH][hapmap];0.92[TSI][hapmap];0.92[EUR][1000 genomes]
rs28594191	0.91[ASN][1000 genomes]
rs35779003	0.96[EUR][1000 genomes]
rs3772636	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3821502	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4441681	0.92[EUR][1000 genomes]
rs4569682	0.95[CEU][hapmap];0.95[EUR][1000 genomes]
rs4894257	0.96[EUR][1000 genomes]
rs4894258	0.96[EUR][1000 genomes]
rs4894280	0.87[EUR][1000 genomes]
rs4894286	0.96[CEU][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs4894287	0.88[CEU][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes]
rs4894289	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4894290	0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6439561	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6763009	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6766459	0.85[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs6799448	0.88[CEU][hapmap];0.92[EUR][1000 genomes]
rs6799471	0.92[CEU][hapmap];0.92[EUR][1000 genomes]
rs875368	0.96[EUR][1000 genomes]
rs875369	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs882060	0.96[EUR][1000 genomes]
rs9822213	0.96[CEU][hapmap];0.87[GIH][hapmap];0.92[TSI][hapmap];0.95[EUR][1000 genomes]
rs9824249	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9837009	0.93[EUR][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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6776570	TXNDC6	cis	cerebellum	SCAN
rs6776570	CEP63	cis	parietal	SCAN
rs6776570	KY	cis	cerebellum	SCAN
rs6776570	SLC38A2	trans	parietal	SCAN
rs6776570	PPP2R3A	cis	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:134885600-134912200	Weak transcription	Brain Germinal Matrix	brain
2	chr3:134889000-134924600	Weak transcription	Brain Anterior Caudate	brain
3	chr3:134895800-134912000	Weak transcription	Brain Angular Gyrus	brain
4	chr3:134907200-134913400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
5	chr3:134907400-134922400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:134909000-134932400	Weak transcription	Psoas Muscle	Psoas
7	chr3:134909800-134912200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr3:134910000-134913600	Weak transcription	Fetal Muscle Trunk	muscle
9	chr3:134910000-134914800	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr3:134910000-134926400	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr3:134910200-134923400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr3:134910800-134932600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr3:134911000-134922000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr3:134911400-134912600	Enhancers	Brain Cingulate Gyrus	brain
15	chr3:134911400-134912600	Enhancers	Brain Substantia Nigra	brain
16	chr3:134911400-134912800	Enhancers	Brain Hippocampus Middle	brain
17	chr3:134911400-134913600	Strong transcription	Fetal Brain Female	brain
18	chr3:134911600-134912600	Enhancers	Brain Inferior Temporal Lobe	brain
19	chr3:134911800-134912600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain

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