Variant report

Variant	rs6664279
Chromosome Location	chr1:113914023-113914024
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:113908670..113911236-chr1:113911521..113914710,4	K562	blood:
2	chr1:113912898..113914605-chr1:113928576..113931565,2	MCF-7	breast:
3	chr1:113911404..113914976-chr1:113918740..113920937,3	MCF-7	breast:

Extended variants
information (count: 40 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10494160	0.86[ASN][1000 genomes]
rs10857991	0.83[ASN][1000 genomes]
rs11102613	0.81[ASN][1000 genomes]
rs12022522	0.81[ASN][1000 genomes]
rs12022558	0.81[ASN][1000 genomes]
rs12027464	0.86[ASN][1000 genomes]
rs12028292	0.86[ASN][1000 genomes]
rs12028450	0.83[ASN][1000 genomes]
rs12029185	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12031069	0.86[CHB][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs12031201	0.86[ASN][1000 genomes]
rs12032132	0.85[ASN][1000 genomes]
rs12032137	0.85[ASN][1000 genomes]
rs12032749	0.86[ASN][1000 genomes]
rs12033092	0.83[JPT][hapmap]
rs12033935	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12034394	0.86[ASN][1000 genomes]
rs12034896	0.86[ASN][1000 genomes]
rs12035230	0.85[ASN][1000 genomes]
rs12037686	0.86[ASN][1000 genomes]
rs12047722	0.81[ASN][1000 genomes]
rs12734784	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17013288	0.86[ASN][1000 genomes]
rs17031447	0.86[ASN][1000 genomes]
rs17031448	0.86[ASN][1000 genomes]
rs35862767	0.86[ASN][1000 genomes]
rs4838983	0.81[ASN][1000 genomes]
rs4839309	0.81[ASN][1000 genomes]
rs4839316	0.86[ASN][1000 genomes]
rs4839317	0.86[ASN][1000 genomes]
rs6688827	0.83[ASW][hapmap]
rs7525945	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427719	chr1:113570229-114078388	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	nsv999873	chr1:113840351-113949453	Enhancers Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases
3	nsv1009534	chr1:113856612-113920889	Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv1010110	chr1:113856612-113969417	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases
5	nsv1013228	chr1:113861524-113919893	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv1005599	chr1:113861524-113920889	Weak transcription Active TSS Enhancers Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv1012143	chr1:113861524-113930779	Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
8	nsv1014757	chr1:113861524-113969417	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6664279	CD58	cis	cerebellum	SCAN
rs6664279	SYT6	cis	parietal	SCAN
rs6664279	ALX3	cis	cerebellum	SCAN
rs6664279	DENND2C	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113912000-113914800	Weak transcription	Primary T cells from cord blood	blood
2	chr1:113913200-113918600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:113913800-113915000	Enhancers	HepG2	liver

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