Variant report

Variant	rs16842498
Chromosome Location	chr4:8539529-8539530
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:8538338..8543611-chr4:8548493..8553766,7	MCF-7	breast:
2	chr4:8469952..8472230-chr4:8539162..8541122,2	MCF-7	breast:
3	chr4:8534354..8538693-chr4:8538746..8544060,9	MCF-7	breast:

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs13139429	0.80[AMR][1000 genomes]
rs13140128	0.89[ASN][1000 genomes]
rs16842480	0.90[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16842483	0.81[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.92[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs16842486	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16842557	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16842560	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16842563	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16842567	0.90[CHB][hapmap];0.84[ASN][1000 genomes]
rs3103082	0.94[ASN][1000 genomes]
rs4247232	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4247233	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4259044	0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4358384	0.99[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4619877	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4696692	0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4696693	0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4696695	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4696696	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4696838	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55765509	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55789011	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55977448	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56053534	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61258495	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs62287446	0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs62287448	0.84[EUR][1000 genomes]
rs62287455	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs869600	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs869602	0.99[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs883607	0.81[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16842498	RP11-689P11.2	cis	lung	GTEx

Chromatin state (count:40 , 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	chr4:8535000-8541600	Enhancers	Pancreas	Pancrea
4	chr4:8535800-8540400	Enhancers	Lung	lung
5	chr4:8536000-8541400	Enhancers	Stomach Mucosa	stomach
6	chr4:8536600-8541400	Enhancers	Esophagus	oesophagus
7	chr4:8536800-8539600	Enhancers	Fetal Thymus	thymus
8	chr4:8537400-8539800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
9	chr4:8537400-8542200	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr4:8537600-8542600	Enhancers	GM12878-XiMat	blood
11	chr4:8538200-8541600	Enhancers	HMEC	breast
12	chr4:8538200-8542200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr4:8538200-8542200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr4:8538400-8541200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr4:8538400-8541200	Enhancers	Osteobl	bone
16	chr4:8538400-8542200	Enhancers	NHDF-Ad	bronchial
17	chr4:8538600-8539600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr4:8538600-8539600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr4:8538600-8539600	Enhancers	Gastric	stomach
20	chr4:8538600-8539600	Enhancers	NHEK	skin
21	chr4:8538600-8539800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr4:8538600-8541200	Enhancers	HSMM	muscle
23	chr4:8538600-8541200	Enhancers	NHLF	lung
24	chr4:8538600-8542200	Enhancers	Muscle Satellite Cultured Cells	--
25	chr4:8538800-8541000	Enhancers	A549	lung
26	chr4:8538800-8541200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr4:8538800-8541800	Enhancers	Placenta Amnion	Placenta Amnion
28	chr4:8539000-8539600	Enhancers	NH-A	brain
29	chr4:8539000-8541400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr4:8539000-8541400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr4:8539200-8539600	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
32	chr4:8539200-8539600	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr4:8539200-8540400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr4:8539200-8542200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr4:8539400-8539600	Enhancers	Stomach Smooth Muscle	stomach
36	chr4:8539400-8539600	Active TSS	Hela-S3	cervix
37	chr4:8539400-8540800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr4:8539400-8541000	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr4:8539400-8541800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr4:8539400-8546400	Weak transcription	HSMMtube	muscle

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