Variant report

Variant	rs17161476
Chromosome Location	chr5:108065499-108065500
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chr5:108065366-108065539	MCF10A-Er-Src	breast:	n/a	chr5:108065442-108065453
2	CEBPB	chr5:108063229-108065583	Hela-S3	cervix:	n/a	chr5:108065188-108065201 chr5:108065190-108065199 chr5:108065190-108065199 chr5:108065190-108065199 chr5:108065138-108065147 chr5:108065188-108065199 chr5:108065136-108065147 chr5:108065188-108065201 chr5:108065138-108065147 chr5:108065138-108065147

No.	Distal block	Cell Line	Cell type
1	chr5:108060235..108074407-chr5:108078172..108087811,48	K562	blood:
2	chr5:108062598..108065696-chr5:108743430..108747045,3	K562	blood:
3	chr5:108062273..108066431-chr5:108081834..108086243,5	MCF-7	breast:
4	chr5:108062575..108065883-chr5:108081229..108085721,5	MCF-7	breast:
5	chr5:108059312..108068052-chr5:108079113..108087366,42	K562	blood:

Variant related genes	Relation type
LINC01023	TF binding region
ENSG00000151422	Chromatin interaction
ENSG00000198961	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10038669	0.92[JPT][hapmap]
rs10062204	0.85[JPT][hapmap]
rs10063167	0.92[JPT][hapmap]
rs10066173	0.80[AMR][1000 genomes]
rs10073668	0.92[JPT][hapmap]
rs1022045	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1109617	0.90[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11240982	0.81[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11739006	0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12153703	0.82[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs13173714	0.90[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs13180513	0.92[JPT][hapmap]
rs1423456	0.81[CEU][hapmap];0.94[TSI][hapmap];0.80[AMR][1000 genomes]
rs1423457	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2081126	0.92[JPT][hapmap]
rs2081129	0.92[JPT][hapmap]
rs2900035	0.92[JPT][hapmap]
rs34660781	0.93[ASN][1000 genomes]
rs35398495	0.94[ASN][1000 genomes]
rs3805601	0.82[TSI][hapmap]
rs4957789	0.90[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6594333	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6594334	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6594336	0.82[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6869591	0.81[CEU][hapmap];0.87[TSI][hapmap]
rs6871143	0.82[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6871239	0.82[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6873068	0.94[ASN][1000 genomes]
rs6874229	0.92[JPT][hapmap]
rs6880284	0.92[JPT][hapmap]
rs6889967	0.82[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6891194	0.92[JPT][hapmap]
rs6892439	0.97[ASN][1000 genomes]
rs6895027	0.92[JPT][hapmap]
rs7712834	0.92[JPT][hapmap]
rs7716320	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7716485	0.97[ASN][1000 genomes]
rs7716498	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7735235	0.92[JPT][hapmap]
rs9285863	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9326748	0.92[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv882689	chr5:107595383-108299744	Enhancers ZNF genes & repeats Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:108063400-108065600	Active TSS	Breast Myoepithelial Primary Cells	Breast
2	chr5:108064400-108065600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr5:108064600-108066200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr5:108064600-108071600	Weak transcription	Pancreas	Pancrea
5	chr5:108064800-108065800	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr5:108064800-108065800	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr5:108064800-108066000	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr5:108064800-108066000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr5:108064800-108066200	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr5:108064800-108066200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr5:108065000-108066000	Enhancers	Hela-S3	cervix
12	chr5:108065000-108066200	Weak transcription	NHDF-Ad	bronchial
13	chr5:108065000-108066200	Enhancers	NHEK	skin
14	chr5:108065000-108066400	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr5:108065000-108066600	Enhancers	Primary B cells from peripheral blood	blood
16	chr5:108065000-108068400	Enhancers	Primary monocytes fromperipheralblood	blood
17	chr5:108065200-108065600	Enhancers	Primary hematopoietic stem cells	blood
18	chr5:108065200-108065600	Weak transcription	HUVEC	blood vessel
19	chr5:108065200-108066000	Enhancers	HMEC	breast
20	chr5:108065200-108067400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr5:108065200-108067400	Enhancers	Primary B cells from cord blood	blood
22	chr5:108065200-108068400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr5:108065400-108065600	Enhancers	Fetal Lung	lung
24	chr5:108065400-108066000	Enhancers	K562	blood
25	chr5:108065400-108066600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr5:108065400-108067200	Enhancers	Monocytes-CD14+_RO01746	blood
27	chr5:108065400-108067400	Enhancers	GM12878-XiMat	blood

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