Variant report

Variant	rs12297690
Chromosome Location	chr12:33333954-33333955
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:33332688..33334476-chr12:33590436..33592933,2	MCF-7	breast:
2	chr12:33333640..33335661-chr12:33603103..33604823,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000110975	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10047666	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];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10506104	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10772037	0.83[EUR][1000 genomes]
rs10772040	0.91[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs10844471	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10844474	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10844480	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10844483	0.82[AFR][1000 genomes]
rs10844491	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10844492	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs11052480	0.82[AFR][1000 genomes]
rs11052501	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11052502	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11052503	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11052526	0.90[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs1392331	1.00[CEU][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs1445311	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1961179	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1961180	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2120967	0.91[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs59547881	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72640193	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530421	chr12:32825335-33465991	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv558218	chr12:33302438-33334261	Weak transcription ZNF genes & repeats Enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv1037459	chr12:33310703-33905662	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv541459	chr12:33310703-33905662	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv1054927	chr12:33325003-33379954	Enhancers ZNF genes & repeats Weak transcription Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv519988	chr12:33332749-33337457	Weak transcription Enhancers Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:33331600-33334600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr12:33333200-33335400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr12:33333400-33334200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr12:33333600-33334000	Enhancers	Placenta Amnion	Placenta Amnion

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