Variant report

Variant	rs561233
Chromosome Location	chr1:179906900-179906901
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:179906513..179911873-chr1:179922155..179925771,5	K562	blood:
2	chr1:179899680..179902372-chr1:179905754..179907325,2	K562	blood:
3	chr1:179850926..179852499-chr1:179905146..179907597,2	MCF-7	breast:
4	chr1:179896181..179898748-chr1:179905765..179908705,2	MCF-7	breast:
5	chr1:179898424..179901062-chr1:179905240..179907123,2	MCF-7	breast:
6	chr1:179901782..179903357-chr1:179905596..179908288,2	K562	blood:
7	chr1:179906042..179908013-chr1:179920844..179923760,2	K562	blood:

Variant related genes	Relation type
ENSG00000135837	Chromatin interaction
ENSG00000260360	Chromatin interaction
ENSG00000272906	Chromatin interaction
ENSG00000143337	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10913916	0.93[JPT][hapmap]
rs10913917	0.81[JPT][hapmap]
rs10913918	0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs12091685	0.82[CHD][hapmap]
rs1281384	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1281386	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1281389	0.88[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1297205	0.80[CEU][hapmap];0.88[CHB][hapmap];0.93[JPT][hapmap]
rs2281805	0.88[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2319676	0.83[JPT][hapmap]
rs2319677	0.86[JPT][hapmap]
rs2477106	0.87[JPT][hapmap]
rs2477111	0.81[JPT][hapmap]
rs2477112	0.81[JPT][hapmap]
rs2477114	0.81[ASN][1000 genomes]
rs2477118	0.81[JPT][hapmap]
rs2477119	0.86[JPT][hapmap]
rs2483622	0.87[JPT][hapmap]
rs2501608	0.87[JPT][hapmap]
rs2501611	0.81[JPT][hapmap]
rs2501613	0.81[JPT][hapmap]
rs2501615	0.82[CEU][hapmap];0.81[JPT][hapmap]
rs2501621	0.87[JPT][hapmap]
rs2762859	0.81[JPT][hapmap]
rs2777910	0.88[CHB][hapmap];0.89[CHD][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs2985373	0.92[ASN][1000 genomes]
rs4147170	0.86[JPT][hapmap]
rs4622030	0.86[JPT][hapmap]
rs4652470	0.82[CHD][hapmap]
rs483307	0.81[JPT][hapmap]
rs500371	0.88[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap]
rs504202	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs510209	0.81[JPT][hapmap]
rs511332	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs521858	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs526683	0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs528350	0.81[CEU][hapmap];0.89[CHB][hapmap];0.93[JPT][hapmap]
rs533795	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs534168	0.81[CEU][hapmap];0.89[CHB][hapmap];0.93[JPT][hapmap]
rs539324	0.83[ASN][1000 genomes]
rs551607	0.88[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs552743	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs552763	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs571822	0.84[AFR][1000 genomes]
rs585355	0.88[CHB][hapmap];0.89[CHD][hapmap];0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs6425606	0.82[CHD][hapmap];0.85[JPT][hapmap]
rs6425607	0.86[JPT][hapmap]
rs7521895	1.00[JPT][hapmap]

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	nsv429936	chr1:179790343-180214343	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv429947	chr1:179790518-179925104	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	esv1815608	chr1:179813499-180067988	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	nsv429958	chr1:179814306-179994628	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179902000-179907800	Weak transcription	Stomach Mucosa	stomach
2	chr1:179905000-179907000	Enhancers	GM12878-XiMat	blood
3	chr1:179905800-179910600	Weak transcription	K562	blood
4	chr1:179906800-179907400	Enhancers	Muscle Satellite Cultured Cells	--
5	chr1:179906800-179909400	Enhancers	Hela-S3	cervix

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