Variant report

Variant	rs1934629
Chromosome Location	chr1:210914747-210914748
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:210913946..210916328-chr1:210919386..210921041,2	MCF-7	breast:

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1770213	1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1770216	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1770219	0.90[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap]
rs1777243	0.86[JPT][hapmap];0.82[EUR][1000 genomes]
rs1777245	0.91[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1777258	1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs1777260	0.82[EUR][1000 genomes]
rs1777261	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1777264	0.91[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1890839	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1890840	0.91[GIH][hapmap];0.86[JPT][hapmap];0.94[MEX][hapmap];0.82[EUR][1000 genomes]
rs1890844	0.81[JPT][hapmap]
rs1890845	1.00[CHB][hapmap];0.85[CHD][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs1890847	0.92[CHB][hapmap]
rs1934628	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1934630	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1934636	1.00[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2884390	1.00[CHB][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs4405188	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4951564	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4951615	0.86[JPT][hapmap]
rs6665563	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7514108	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7515909	0.86[GIH][hapmap];0.94[MEX][hapmap]
rs7546472	0.82[GIH][hapmap];0.88[MEX][hapmap]
rs9429846	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9429847	0.92[CEU][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873148	chr1:210665583-210994339	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	nsv873153	chr1:210900481-210994339	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
3	nsv999018	chr1:210907239-210999306	Genic enhancers Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1934629	BATF3	cis	parietal	SCAN
rs1934629	DTL	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:210871200-210932000	Weak transcription	HSMM	muscle
2	chr1:210903800-210919200	Weak transcription	HSMMtube	muscle
3	chr1:210905600-210921200	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr1:210910600-210921200	Weak transcription	Brain Angular Gyrus	brain

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