Variant report

Variant	rs6856478
Chromosome Location	chr4:56551916-56551917
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	chr4:56501880..56503647-chr4:56551680..56553889,2	K562	blood:
2	chr4:56550080..56552632-chr4:56586091..56588809,2	K562	blood:

Variant related genes	Relation type
ENSG00000109255	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs12510765	1.00[ASN][1000 genomes]
rs4333263	1.00[ASN][1000 genomes]
rs4412048	1.00[ASN][1000 genomes]
rs4631105	1.00[ASN][1000 genomes]
rs4864552	1.00[ASN][1000 genomes]
rs4864562	1.00[ASN][1000 genomes]
rs4865031	1.00[ASN][1000 genomes]
rs6554281	1.00[ASN][1000 genomes]
rs6554299	1.00[CEU][hapmap];0.94[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6554309	1.00[ASN][1000 genomes]
rs6554311	1.00[ASN][1000 genomes]
rs6554312	1.00[ASN][1000 genomes]
rs6554314	1.00[ASN][1000 genomes]
rs6554317	1.00[ASN][1000 genomes]
rs6828640	1.00[ASN][1000 genomes]
rs6838362	1.00[ASN][1000 genomes]
rs6842779	1.00[ASN][1000 genomes]
rs73236158	1.00[ASN][1000 genomes]
rs7668437	1.00[ASN][1000 genomes]
rs7678383	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7691573	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2755990	chr4:56317136-57143037	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	nsv10496	chr4:56336946-56841137	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	nsv998179	chr4:56425126-56694339	Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv932636	chr4:56438618-56667329	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv879021	chr4:56482750-56648713	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv1006944	chr4:56512574-56580169	Enhancers Active TSS Weak transcription Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv1005845	chr4:56522075-56980357	Active TSS Bivalent Enhancer Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6856478	CLOCK	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:56551800-56552400	Enhancers	H9 Cell Line	embryonic stem cell
2	chr4:56551800-56552400	Enhancers	iPS-18 Cell Line	embryonic stem cell

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