Variant report

Variant	rs1288
Chromosome Location	chr12:66846788-66846789
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:66843010..66844547-chr12:66845605..66847114,2	MCF-7	breast:

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1038923	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10784538	0.84[EUR][1000 genomes]
rs10784539	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10784540	0.80[AMR][1000 genomes]
rs10784541	0.87[ASN][1000 genomes]
rs10784545	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11176191	0.90[ASN][1000 genomes]
rs11176204	0.86[JPT][hapmap]
rs11176205	0.82[JPT][hapmap]
rs11609808	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12099798	0.82[YRI][hapmap]
rs12321126	0.88[ASN][1000 genomes]
rs1845296	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3891951	0.85[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4913307	0.84[EUR][1000 genomes]
rs4913310	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4913496	0.84[EUR][1000 genomes]
rs4913502	0.84[ASN][1000 genomes]
rs6581698	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7132569	0.86[JPT][hapmap]
rs7135061	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7307274	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7487758	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7952846	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7960332	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7962122	0.87[ASN][1000 genomes]
rs9989032	0.80[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[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	nsv1052503	chr12:66293898-67269495	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv541515	chr12:66293898-67269495	Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv1051713	chr12:66745716-66889411	Strong transcription Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv1040682	chr12:66750103-67328053	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv832447	chr12:66785814-66990029	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:66823200-66859000	Weak transcription	Brain Germinal Matrix	brain
2	chr12:66836000-66846800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr12:66836200-66849200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:66836200-66849400	Weak transcription	Fetal Kidney	kidney
5	chr12:66836200-66856600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr12:66836400-66855200	Weak transcription	Placenta	Placenta
7	chr12:66837200-66849200	Weak transcription	Brain Anterior Caudate	brain
8	chr12:66838800-66858400	Weak transcription	Fetal Brain Female	brain
9	chr12:66842800-66849200	Weak transcription	Esophagus	oesophagus
10	chr12:66843400-66849600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr12:66843800-66857200	Weak transcription	HMEC	breast
12	chr12:66844000-66861600	Weak transcription	Primary T cells from cord blood	blood
13	chr12:66845800-66846800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr12:66845800-66847600	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr12:66846200-66847200	Enhancers	iPS-15b Cell Line	embryonic stem cell

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