Variant report

Variant	rs16842563
Chromosome Location	chr4:8545146-8545147
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:8544571..8547692-chr4:8551879..8553723,3	K562	blood:
2	chr4:8544480..8546948-chr4:8548054..8550987,2	K562	blood:
3	chr4:8542053..8545358-chr4:8547295..8551816,4	MCF-7	breast:
4	chr4:8542415..8545187-chr4:8582095..8584312,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000155269	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs13140128	0.87[ASN][1000 genomes]
rs16842480	0.86[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];0.97[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16842483	0.95[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs16842486	0.82[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.81[TSI][hapmap];0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs16842498	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16842557	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16842560	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16842567	0.91[CHB][hapmap];0.86[ASN][1000 genomes]
rs3103082	0.92[ASN][1000 genomes]
rs4247232	0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4247233	0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4259044	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4358384	0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4619877	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4696692	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4696693	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4696695	0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4696696	0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4696838	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55765509	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55789011	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55977448	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56053534	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61258495	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs62287446	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs62287455	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs869600	0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs869602	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs883607	0.82[CHB][hapmap];0.91[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];0.81[TSI][hapmap];0.89[AMR][1000 genomes];0.82[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	nsv878604	chr4:8315938-8618916	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv1002680	chr4:8357163-8721214	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv4224	chr4:8503727-8546462	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv461221	chr4:8534283-8554894	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv593640	chr4:8534283-8554894	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv878612	chr4:8534283-8618916	Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	esv1832730	chr4:8541086-9514568	Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
8	esv1843578	chr4:8541086-9514568	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16842563	C4orf23	cis	parietal	SCAN
rs16842563	C4orf23	cis	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:8539400-8546400	Weak transcription	HSMMtube	muscle
2	chr4:8539600-8546400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr4:8541200-8546000	Weak transcription	HSMM	muscle
4	chr4:8541600-8549000	Weak transcription	HMEC	breast
5	chr4:8541800-8545800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr4:8542200-8546200	Weak transcription	Osteobl	bone
7	chr4:8542200-8546400	Weak transcription	NHLF	lung
8	chr4:8542200-8548800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr4:8544000-8545400	Enhancers	NHDF-Ad	bronchial
10	chr4:8544400-8546600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr4:8544400-8551600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr4:8544400-8552600	Enhancers	Placenta	Placenta
13	chr4:8544600-8546000	Enhancers	Esophagus	oesophagus
14	chr4:8544800-8545200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr4:8544800-8549600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr4:8544800-8556600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr4:8545000-8546200	Weak transcription	Spleen	Spleen
18	chr4:8545000-8547200	Weak transcription	H1 Cell Line	embryonic stem cell

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