Variant report

Variant	rs16842486
Chromosome Location	chr4:8537786-8537787
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:8473542..8475287-chr4:8537371..8538949,2	MCF-7	breast:
2	chr4:8521151..8523574-chr4:8535830..8537925,2	MCF-7	breast:
3	chr4:8537532..8539229-chr4:8550769..8552595,2	MCF-7	breast:
4	chr4:8534354..8538693-chr4:8538746..8544060,9	MCF-7	breast:
5	chr4:8531043..8532660-chr4:8536787..8539068,2	K562	blood:
6	chr4:8535273..8538017-chr4:8547280..8549775,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000155275	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs13139429	0.87[AMR][1000 genomes]
rs13140128	0.90[ASN][1000 genomes]
rs16842480	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.88[TSI][hapmap];0.92[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs16842483	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16842498	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16842557	0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs16842560	0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs16842563	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]
rs16842567	0.87[CHB][hapmap];0.82[ASN][1000 genomes]
rs3103082	0.96[ASN][1000 genomes]
rs4247232	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4247233	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4259044	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4358384	0.91[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4619877	0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4696692	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4696693	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4696695	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4696696	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4696838	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55765509	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55789011	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55977448	0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs56053534	0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs61258495	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62287446	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62287455	0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs869600	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs869602	0.91[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs883607	0.95[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[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	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	nsv980117	chr4:8535043-8545141	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16842486	C4orf23	cis	cerebellum	SCAN
rs16842486	C4orf23	cis	parietal	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:8532600-8542800	Enhancers	Placenta	Placenta
2	chr4:8533200-8542800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr4:8533800-8537800	Enhancers	H1 Cell Line	embryonic stem cell
4	chr4:8535000-8541600	Enhancers	Pancreas	Pancrea
5	chr4:8535200-8538600	Enhancers	Colon Smooth Muscle	Colon
6	chr4:8535600-8538000	Enhancers	Fetal Kidney	kidney
7	chr4:8535800-8540400	Enhancers	Lung	lung
8	chr4:8536000-8537800	Enhancers	iPS-18 Cell Line	embryonic stem cell
9	chr4:8536000-8538200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr4:8536000-8538600	Weak transcription	Fetal Lung	lung
11	chr4:8536000-8538600	Weak transcription	Fetal Stomach	stomach
12	chr4:8536000-8538600	Weak transcription	Gastric	stomach
13	chr4:8536000-8538600	Weak transcription	Ovary	ovary
14	chr4:8536000-8538800	Weak transcription	Colonic Mucosa	Colon
15	chr4:8536000-8541400	Enhancers	Stomach Mucosa	stomach
16	chr4:8536400-8537800	Weak transcription	Rectal Smooth Muscle	rectum
17	chr4:8536400-8538400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr4:8536600-8538200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr4:8536600-8538400	Weak transcription	HSMMtube	muscle
20	chr4:8536600-8538600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr4:8536600-8538600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr4:8536600-8538600	Weak transcription	NHEK	skin
23	chr4:8536600-8538800	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr4:8536600-8541400	Enhancers	Esophagus	oesophagus
25	chr4:8536800-8538200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr4:8536800-8538200	Weak transcription	HMEC	breast
27	chr4:8536800-8538600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr4:8536800-8538800	Weak transcription	Duodenum Mucosa	Duodenum
29	chr4:8536800-8538800	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr4:8536800-8539600	Enhancers	Fetal Thymus	thymus
31	chr4:8537000-8538800	Enhancers	Stomach Smooth Muscle	stomach
32	chr4:8537200-8537800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr4:8537200-8537800	Enhancers	Duodenum Smooth Muscle	Duodenum
34	chr4:8537200-8538800	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr4:8537400-8538600	Weak transcription	Fetal Intestine Large	intestine
36	chr4:8537400-8538800	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr4:8537400-8539800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
38	chr4:8537400-8542200	Enhancers	Breast Myoepithelial Primary Cells	Breast
39	chr4:8537600-8542600	Enhancers	GM12878-XiMat	blood

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