Variant report

Variant	rs1546277
Chromosome Location	chr1:211111969-211111970
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	chr1:211109430..211112551-chr1:211113877..211116492,3	K562	blood:

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

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

rs_ID	r²[population]
rs10779548	0.92[ASW][hapmap]
rs10863871	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11119636	0.88[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11119639	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1501553	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1501554	0.96[CEU][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1501561	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1566602	0.96[CEU][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1777242	0.81[CEU][hapmap]
rs2062673	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2088877	0.81[EUR][1000 genomes]
rs2102129	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2202095	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2358092	0.96[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2358115	0.80[AMR][1000 genomes]
rs2358117	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4639824	0.82[EUR][1000 genomes]
rs4951491	0.81[CEU][hapmap]
rs4951700	0.87[EUR][1000 genomes]
rs4951701	0.96[CEU][hapmap];1.00[GIH][hapmap];0.96[MEX][hapmap];0.87[MKK][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4951704	0.95[CEU][hapmap]
rs6686447	0.91[CEU][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6702809	0.96[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7415388	0.82[EUR][1000 genomes]
rs924567	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs924568	0.96[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.87[MKK][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs973945	0.80[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873154	chr1:211057697-211117197	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1546277	C1orf74	cis	parietal	SCAN
rs1546277	IKBKE	cis	parietal	SCAN
rs1546277	CD46	cis	cerebellum	SCAN
rs1546277	SERTAD4	cis	cerebellum	SCAN
rs1546277	NSL1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:211108600-211117400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr1:211110400-211112200	Enhancers	HSMMtube	muscle
3	chr1:211110800-211112400	Enhancers	HSMM	muscle
4	chr1:211111200-211112200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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