Variant report

Variant	rs12348055
Chromosome Location	chr9:107939579-107939580
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:107934852..107940602-chr9:108005690..108009154,7	MCF-7	breast:
2	chr18:42706846..42707691-chr9:107939420..107940374,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000070214	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10521072	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10991570	1.00[CHB][hapmap]
rs10991572	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10991573	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10991575	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10991576	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10991580	1.00[CHB][hapmap]
rs10991581	1.00[CHB][hapmap]
rs10991582	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10991600	1.00[CEU][hapmap]
rs10991618	1.00[CEU][hapmap]
rs12335779	1.00[CEU][hapmap]
rs12337995	0.82[EUR][1000 genomes]
rs12343550	0.82[EUR][1000 genomes]
rs12345601	1.00[CEU][hapmap]
rs12347331	0.82[EUR][1000 genomes]
rs12347364	1.00[CEU][hapmap]
rs12347579	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12348359	0.82[EUR][1000 genomes]
rs12350390	0.82[EUR][1000 genomes]
rs12352127	0.82[EUR][1000 genomes]
rs12353489	0.82[EUR][1000 genomes]
rs28541268	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs66546819	0.82[EUR][1000 genomes]
rs66692440	0.82[EUR][1000 genomes]
rs66850568	0.82[EUR][1000 genomes]
rs67361890	0.82[EUR][1000 genomes]
rs67751791	0.82[EUR][1000 genomes]
rs67803665	0.82[EUR][1000 genomes]
rs67935728	0.82[EUR][1000 genomes]
rs68102455	0.82[EUR][1000 genomes]
rs72607136	0.82[EUR][1000 genomes]
rs73506445	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73508509	0.82[EUR][1000 genomes]
rs7865517	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9886744	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[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	nsv1046935	chr9:107414720-108028061	Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv1045108	chr9:107509553-108188550	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv893684	chr9:107893629-108001107	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv831678	chr9:107923522-108112813	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv1045079	chr9:107938039-107975595	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 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	chr9:107936000-107939800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr9:107936200-107939800	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr9:107936600-107943600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr9:107939000-107940600	Enhancers	Brain Germinal Matrix	brain

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