Variant report

Variant	rs16842480
Chromosome Location	chr4:8535621-8535622
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:8483624..8484422-chr4:8535583..8536138,2	MCF-7	breast:
2	chr4:8480343..8482118-chr4:8533933..8535799,2	MCF-7	breast:
3	chr4:8534354..8538693-chr4:8538746..8544060,9	MCF-7	breast:
4	chr4:8499557..8501918-chr4:8533819..8536050,2	MCF-7	breast:
5	chr4:8495654..8498484-chr4:8534530..8537327,2	MCF-7	breast:
6	chr4:8534257..8535987-chr4:8582200..8584204,2	MCF-7	breast:
7	chr4:8519832..8523485-chr4:8533626..8535724,3	MCF-7	breast:
8	chr4:8535273..8538017-chr4:8547280..8549775,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000205959	Chromatin interaction
ENSG00000155269	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs13139429	0.80[AMR][1000 genomes]
rs13140128	0.94[ASN][1000 genomes]
rs16842483	0.81[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16842486	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]
rs16842498	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16842557	0.97[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16842560	0.97[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16842563	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]
rs16842567	0.87[CHB][hapmap]
rs3103082	0.99[ASN][1000 genomes]
rs4247232	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4247233	0.91[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4259044	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4358384	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4619877	0.97[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4696692	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4696693	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4696695	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4696696	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4696838	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55765509	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55789011	0.92[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs55977448	0.97[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56053534	0.97[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61258495	0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs62287446	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62287455	0.97[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs869600	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs869602	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs883607	0.81[ASW][hapmap];0.82[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.96[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs16842480	C4orf23	cis	cerebellum	SCAN
rs16842480	RP11-689P11.2	cis	lung	GTEx
rs16842480	C4orf23	cis	parietal	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:8532400-8535800	Weak transcription	NHDF-Ad	bronchial
2	chr4:8532600-8542800	Enhancers	Placenta	Placenta
3	chr4:8533200-8542800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr4:8533600-8537400	Enhancers	Placenta Amnion	Placenta Amnion
5	chr4:8533800-8537800	Enhancers	H1 Cell Line	embryonic stem cell
6	chr4:8534600-8536000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr4:8534800-8536800	Weak transcription	Fetal Thymus	thymus
8	chr4:8535000-8535800	Enhancers	iPS-20b Cell Line	embryonic stem cell
9	chr4:8535000-8536600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr4:8535000-8537000	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr4:8535000-8537200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr4:8535000-8541600	Enhancers	Pancreas	Pancrea
13	chr4:8535200-8536600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr4:8535200-8536800	Enhancers	Fetal Intestine Small	intestine
15	chr4:8535200-8537400	Enhancers	H9 Cell Line	embryonic stem cell
16	chr4:8535200-8537400	Enhancers	Fetal Intestine Large	intestine
17	chr4:8535200-8538600	Enhancers	Colon Smooth Muscle	Colon
18	chr4:8535400-8535800	Enhancers	HUES64 Cell Line	embryonic stem cell
19	chr4:8535400-8535800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr4:8535400-8536000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr4:8535400-8536800	Enhancers	HMEC	breast
22	chr4:8535600-8535800	Enhancers	Duodenum Mucosa	Duodenum
23	chr4:8535600-8535800	Enhancers	Rectal Mucosa Donor 31	rectum
24	chr4:8535600-8535800	Enhancers	Stomach Smooth Muscle	stomach
25	chr4:8535600-8536000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
26	chr4:8535600-8536000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
27	chr4:8535600-8536000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr4:8535600-8536000	Enhancers	Colonic Mucosa	Colon
29	chr4:8535600-8536000	Enhancers	Fetal Lung	lung
30	chr4:8535600-8536000	Enhancers	Gastric	stomach
31	chr4:8535600-8536000	Enhancers	Ovary	ovary
32	chr4:8535600-8536000	Flanking Active TSS	Stomach Mucosa	stomach
33	chr4:8535600-8536000	Flanking Active TSS	GM12878-XiMat	blood
34	chr4:8535600-8536200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr4:8535600-8536200	Enhancers	Esophagus	oesophagus
36	chr4:8535600-8536200	Flanking Active TSS	NHEK	skin
37	chr4:8535600-8536600	Enhancers	HUES6 Cell Line	embryonic stem cell
38	chr4:8535600-8536600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr4:8535600-8536600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
40	chr4:8535600-8536600	Enhancers	Sigmoid Colon	Sigmoid Colon
41	chr4:8535600-8536600	Enhancers	HSMMtube	muscle
42	chr4:8535600-8536800	Enhancers	iPS-15b Cell Line	embryonic stem cell
43	chr4:8535600-8536800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr4:8535600-8538000	Enhancers	Fetal Kidney	kidney

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