Variant report

Variant	rs16854009
Chromosome Location	chr1:179339262-179339263
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:179338705..179340694-chr1:179346963..179349066,2	K562	blood:
2	chr1:179089949..179090868-chr1:179338641..179339706,4	K562	blood:
3	chr1:179332952..179336574-chr1:179337996..179342859,7	MCF-7	breast:
4	chr1:179074263..179075064-chr1:179338590..179339322,3	K562	blood:
5	chr1:179048422..179049068-chr1:179338591..179339827,3	K562	blood:
6	chr1:179260885..179265137-chr1:179333383..179339387,7	MCF-7	breast:
7	chr1:178511480..178512262-chr1:179338579..179339345,2	K562	blood:
8	chr1:179220558..179221464-chr1:179338599..179339569,5	MCF-7	breast:
9	chr1:179220394..179221467-chr1:179338651..179339953,9	MCF-7	breast:
10	chr1:179333390..179336673-chr1:179338029..179341473,3	MCF-7	breast:
11	chr1:179338659..179339560-chr1:179568499..179569458,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000213057	Chromatin interaction
ENSG00000184909	Chromatin interaction
ENSG00000162779	Chromatin interaction
ENSG00000057252	Chromatin interaction
ENSG00000263633	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10494520	0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap]
rs10753191	0.90[JPT][hapmap]
rs10753192	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10798662	0.80[AFR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10798665	0.87[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap]
rs10798670	0.87[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10913731	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10913732	0.93[ASN][1000 genomes]
rs10913733	0.87[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.85[MEX][hapmap];0.81[MKK][hapmap];0.82[YRI][hapmap];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10913734	0.90[JPT][hapmap]
rs10913737	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10913738	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10913742	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10913758	0.86[ASN][1000 genomes]
rs10913806	0.81[CHB][hapmap]
rs12047160	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12073906	0.86[ASN][1000 genomes]
rs12073970	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12097041	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap]
rs12118625	0.86[ASN][1000 genomes]
rs12120123	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs12130876	0.94[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap]
rs12131473	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs12131475	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs12134114	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs12138436	0.94[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap]
rs12138619	0.86[CEU][hapmap];0.93[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12144580	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12405133	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs12405321	0.94[CHB][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap]
rs12408349	0.94[CHB][hapmap]
rs12408477	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs12725126	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs12740455	0.94[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap]
rs12745772	0.94[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap]
rs12759446	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs1329276	0.81[CHB][hapmap]
rs13306731	0.87[CEU][hapmap];0.94[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13374852	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16854229	0.94[CHB][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap]
rs2274623	0.95[JPT][hapmap]
rs2274625	0.95[JPT][hapmap]
rs3753526	0.87[CEU][hapmap];0.90[JPT][hapmap];0.82[YRI][hapmap]
rs4077551	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4077552	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs41315575	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4133136	1.00[CEU][hapmap];0.93[CHB][hapmap];0.88[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs4394601	0.87[ASN][1000 genomes]
rs59334094	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61822772	0.82[ASN][1000 genomes]
rs61824395	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6425537	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6669967	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs9660720	0.86[ASN][1000 genomes]
rs975025	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005278	chr1:179197645-179371395	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	16 gene(s)	inside rSNPs	diseases
2	esv2762031	chr1:179323738-179375197	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
3	nsv518403	chr1:179323919-179371973	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
4	nsv548279	chr1:179323919-179390148	Enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
5	esv33901	chr1:179328708-179344905	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179339200-179339400	Enhancers	Osteobl	bone

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