Variant report

Variant	rs6428397
Chromosome Location	chr1:197331446-197331447
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:197331402..197332938-chr1:197333106..197334632,2	MCF-7	breast:

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

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

rs_ID	r²[population]
rs10801603	0.89[CHB][hapmap];0.87[JPT][hapmap];0.92[ASN][1000 genomes]
rs12126335	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1337167	0.94[CHB][hapmap];0.87[JPT][hapmap]
rs1337168	0.89[CHB][hapmap];0.87[JPT][hapmap]
rs17618358	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2359151	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2476023	0.88[CHB][hapmap];0.87[JPT][hapmap]
rs2759656	0.82[CHB][hapmap];0.87[JPT][hapmap]
rs2786098	0.94[CHB][hapmap];0.87[JPT][hapmap];0.92[ASN][1000 genomes]
rs2786101	0.89[CHB][hapmap];0.87[JPT][hapmap]
rs2786116	0.94[CHB][hapmap];0.87[JPT][hapmap];0.93[ASN][1000 genomes]
rs2786117	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2786119	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2821107	0.88[CHB][hapmap];0.87[JPT][hapmap];0.90[ASN][1000 genomes]
rs2821115	0.87[CHB][hapmap];0.87[JPT][hapmap];0.94[ASN][1000 genomes]
rs2821116	0.89[CHB][hapmap];0.87[JPT][hapmap];0.94[ASN][1000 genomes]
rs2821117	0.88[CHB][hapmap];0.87[JPT][hapmap];0.93[ASN][1000 genomes]
rs2821125	0.89[CHB][hapmap];0.86[JPT][hapmap]
rs3122635	0.83[ASN][1000 genomes]
rs3122636	0.84[ASN][1000 genomes]
rs4915231	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4915525	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4915526	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6664399	0.92[ASN][1000 genomes]
rs7551088	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs949571	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[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	nsv528460	chr1:196542567-197446702	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv1014039	chr1:197311285-197529212	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6428397	CRB1	cis	brain	BrainEAC

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:197324000-197338800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr1:197324000-197347000	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr1:197329800-197333400	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr1:197329800-197336400	Weak transcription	Ovary	ovary
5	chr1:197329800-197336800	Weak transcription	Brain Angular Gyrus	brain
6	chr1:197329800-197338400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr1:197329800-197342400	Weak transcription	Brain Cingulate Gyrus	brain
8	chr1:197330000-197333600	Weak transcription	Brain Anterior Caudate	brain

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