Variant report

Variant	rs12875741
Chromosome Location	chr13:67488634-67488635
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:67483833..67485636-chr13:67488451..67490558,2	MCF-7	breast:

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11618220	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11841902	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12427700	0.92[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12428689	0.84[CEU][hapmap]
rs12429002	0.88[CEU][hapmap];0.85[GIH][hapmap];0.88[TSI][hapmap];0.88[EUR][1000 genomes]
rs12430583	0.92[CEU][hapmap];0.84[GIH][hapmap];0.88[TSI][hapmap];0.95[EUR][1000 genomes]
rs1442006	0.84[CEU][hapmap];0.82[GIH][hapmap];0.85[TSI][hapmap]
rs1530301	0.80[TSI][hapmap]
rs28459050	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34304003	0.88[EUR][1000 genomes]
rs34948729	0.94[ASN][1000 genomes]
rs4884707	0.92[CEU][hapmap];0.94[EUR][1000 genomes]
rs7324151	0.92[CEU][hapmap];0.95[EUR][1000 genomes]
rs9564358	0.92[CEU][hapmap];0.92[GIH][hapmap];0.90[TSI][hapmap];0.95[EUR][1000 genomes]
rs9564359	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9564360	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.90[TSI][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9564361	0.94[ASN][1000 genomes]
rs9564362	0.94[ASN][1000 genomes]
rs9564363	0.92[ASN][1000 genomes]
rs9571679	0.84[CEU][hapmap]
rs9571680	0.88[CEU][hapmap];0.85[GIH][hapmap];0.85[TSI][hapmap]
rs9571685	0.88[EUR][1000 genomes]
rs9571686	0.93[EUR][1000 genomes]
rs9571687	0.92[CEU][hapmap];0.96[EUR][1000 genomes]
rs9571688	0.96[CEU][hapmap];0.94[EUR][1000 genomes]
rs9571691	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9571692	0.94[ASN][1000 genomes]
rs9571693	0.94[ASN][1000 genomes]
rs9571694	0.94[ASN][1000 genomes]
rs9571695	0.85[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs9571696	0.85[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs9592491	0.83[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041133	chr13:66723731-67530595	Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv530605	chr13:67126136-67697306	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1035741	chr13:67212973-68077950	Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv541817	chr13:67212973-68077950	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv523360	chr13:67322714-67520344	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv1051576	chr13:67322747-67520255	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv900406	chr13:67434161-67532205	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv900407	chr13:67434161-67603745	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv562138	chr13:67455787-67511430	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
10	nsv832640	chr13:67460304-67635966	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv428604	chr13:67480426-67645030	Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:67485600-67489600	Weak transcription	Brain Anterior Caudate	brain
2	chr13:67486600-67489800	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr13:67486600-67490000	Weak transcription	Brain Hippocampus Middle	brain
4	chr13:67487200-67489000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr13:67487200-67489400	Enhancers	Primary T cells from cord blood	blood
6	chr13:67487600-67489000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr13:67487600-67490800	Weak transcription	Brain Angular Gyrus	brain
8	chr13:67488000-67489600	Enhancers	Dnd41	blood
9	chr13:67488000-67490000	Enhancers	Primary B cells from cord blood	blood
10	chr13:67488200-67489000	Enhancers	A549	lung
11	chr13:67488400-67489600	Weak transcription	Brain Substantia Nigra	brain
12	chr13:67488600-67489800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr13:67488600-67490000	Enhancers	Brain Cingulate Gyrus	brain

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