Variant report

Variant	rs12199827
Chromosome Location	chr6:54642129-54642130
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:54640508..54643660-chr6:54711207..54713141,3	MCF-7	breast:
2	chr6:54641381..54644333-chr6:54709873..54712755,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168143	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10223546	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10223849	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10440848	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs10456688	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10948852	0.90[ASN][1000 genomes]
rs10948853	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10948862	0.88[CEU][hapmap];0.86[GIH][hapmap];0.81[MEX][hapmap]
rs12191386	0.83[ASW][hapmap];0.85[CEU][hapmap]
rs12194667	0.85[CEU][hapmap]
rs12195438	0.89[CEU][hapmap];0.86[GIH][hapmap];0.90[MEX][hapmap];0.81[TSI][hapmap]
rs12196314	0.90[CEU][hapmap];0.84[EUR][1000 genomes]
rs12203709	0.89[CEU][hapmap];0.86[GIH][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap]
rs12205372	1.00[ASW][hapmap];0.96[CEU][hapmap];0.84[CHB][hapmap];0.82[CHD][hapmap];0.98[GIH][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs12207559	0.89[CEU][hapmap];0.86[GIH][hapmap];0.81[MEX][hapmap];0.81[TSI][hapmap]
rs12216039	0.87[CEU][hapmap]
rs12216186	0.90[ASN][1000 genomes]
rs13195757	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1393779	0.85[CEU][hapmap]
rs1567164	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1827513	0.92[ASN][1000 genomes]
rs2174145	0.96[LWK][hapmap];0.82[MKK][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes]
rs34713378	0.84[EUR][1000 genomes]
rs4712071	0.90[ASN][1000 genomes]
rs4712075	0.89[CEU][hapmap];0.86[GIH][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap]
rs4715480	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4715481	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4715482	0.89[ASN][1000 genomes]
rs4715484	0.85[ASN][1000 genomes]
rs58988305	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62412605	0.93[EUR][1000 genomes]
rs6908940	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6916681	0.80[CEU][hapmap];0.84[YRI][hapmap];0.88[AFR][1000 genomes]
rs6918226	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6922162	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6922543	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6939992	0.89[ASN][1000 genomes]
rs72957572	0.93[EUR][1000 genomes]
rs7452200	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9296768	0.90[ASN][1000 genomes]
rs9296769	0.87[CEU][hapmap]
rs9464138	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9464139	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9474997	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9475001	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs9475004	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9475005	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.87[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9475006	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9475011	0.89[ASN][1000 genomes]
rs9475013	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9475017	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9475021	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9475029	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv885900	chr6:54517968-54852462	Active TSS Bivalent Enhancer Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv885902	chr6:54588069-54656673	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:54641400-54642200	Enhancers	ES-I3 Cell Line	embryonic stem cell
2	chr6:54641400-54642200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
3	chr6:54641800-54642400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr6:54641800-54642600	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr6:54642000-54642400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr6:54642000-54642400	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr6:54642000-54642400	Enhancers	iPS-20b Cell Line	embryonic stem cell
8	chr6:54642000-54642600	Enhancers	iPS-15b Cell Line	embryonic stem cell

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