Variant report

Variant	rs16873554
Chromosome Location	chr6:45579835-45579836
allele	A/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:45574976..45576984-chr6:45578078..45580337,2	K562	blood:

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs12528502	0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12661124	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12663210	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12665637	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1491142	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16873543	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16873550	1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs2020084	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56083876	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57939401	0.81[ASN][1000 genomes]
rs58939587	0.81[ASN][1000 genomes]
rs59074904	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs60540355	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6458449	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6458450	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6458453	0.83[ASN][1000 genomes]
rs6458454	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6458455	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6899443	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6930188	0.84[ASN][1000 genomes]
rs6936365	0.83[ASN][1000 genomes]
rs6938247	0.96[YRI][hapmap];0.86[AFR][1000 genomes]
rs6938489	0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs713270	0.87[ASN][1000 genomes]
rs73457129	0.83[AFR][1000 genomes]
rs73738526	0.83[ASN][1000 genomes]
rs7742335	0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs7752183	0.81[ASN][1000 genomes]
rs7752200	0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7758915	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7759415	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7764338	0.89[YRI][hapmap];0.81[AFR][1000 genomes]
rs7766534	0.81[ASN][1000 genomes]
rs7768962	0.81[ASN][1000 genomes]
rs9296462	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9296463	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9463108	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9472518	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9472521	0.81[ASN][1000 genomes]
rs9472524	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9472525	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9472530	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9472531	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9472534	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028393	chr6:44875558-45822335	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv538211	chr6:44875558-45822335	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv427755	chr6:45474631-45627025	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv532024	chr6:45475088-45982640	Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:45563800-45586200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:45576400-45581000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr6:45576600-45581400	Weak transcription	Small Intestine	intestine
4	chr6:45576800-45581200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr6:45576800-45585000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr6:45577000-45581200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr6:45577000-45581200	Weak transcription	Osteobl	bone
8	chr6:45577400-45581000	Weak transcription	NHEK	skin
9	chr6:45577400-45581200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr6:45577400-45581400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr6:45577600-45580000	Enhancers	Duodenum Mucosa	Duodenum
12	chr6:45577600-45581000	Weak transcription	HMEC	breast
13	chr6:45577800-45581000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr6:45577800-45581200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr6:45577800-45581200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr6:45577800-45581200	Weak transcription	NHDF-Ad	bronchial
17	chr6:45577800-45581400	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr6:45577800-45581400	Weak transcription	HSMM	muscle
19	chr6:45578000-45581200	Weak transcription	NHLF	lung
20	chr6:45578000-45585200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr6:45578400-45581400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr6:45578400-45582400	Weak transcription	Hela-S3	cervix
23	chr6:45579000-45587800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr6:45579400-45581800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr6:45579600-45581200	Weak transcription	Esophagus	oesophagus
26	chr6:45579800-45580000	ZNF genes & repeats	Pancreas	Pancrea
27	chr6:45579800-45581400	Weak transcription	Fetal Kidney	kidney
28	chr6:45579800-45582600	Weak transcription	Fetal Lung	lung

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