Variant report

Variant	rs343480
Chromosome Location	chr9:6023030-6023031
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	chr9:6013852..6016412-chr9:6021043..6023038,3	MCF-7	breast:
2	chr9:6013606..6016921-chr9:6022468..6025086,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137040	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10121480	1.00[CEU][hapmap]
rs10733517	1.00[CEU][hapmap]
rs10733518	0.90[EUR][1000 genomes]
rs10733520	1.00[CEU][hapmap];0.83[YRI][hapmap]
rs10739079	1.00[CEU][hapmap];0.83[YRI][hapmap]
rs10758731	1.00[CEU][hapmap];0.89[YRI][hapmap]
rs10758732	1.00[CEU][hapmap]
rs10758734	1.00[CEU][hapmap]
rs10815330	1.00[CEU][hapmap]
rs10815335	1.00[CEU][hapmap]
rs1331378	1.00[CEU][hapmap]
rs1331379	1.00[CEU][hapmap];0.89[YRI][hapmap]
rs1418740	1.00[CEU][hapmap]
rs16923578	1.00[CEU][hapmap]
rs186913	1.00[CEU][hapmap]
rs2045959	0.83[ASN][1000 genomes]
rs2150703	1.00[CEU][hapmap]
rs2244053	1.00[CEU][hapmap]
rs2244058	1.00[CEU][hapmap]
rs2291055	1.00[CEU][hapmap]
rs2381360	1.00[CEU][hapmap]
rs2773340	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2773341	1.00[EUR][1000 genomes]
rs343469	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs343471	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap]
rs343482	1.00[CEU][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs343483	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs343500	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3739649	1.00[CEU][hapmap];0.88[YRI][hapmap]
rs404267	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4075225	1.00[CEU][hapmap]
rs419595	0.90[EUR][1000 genomes]
rs4265236	1.00[CEU][hapmap]
rs4389996	1.00[CEU][hapmap]
rs4395943	1.00[CEU][hapmap];0.83[YRI][hapmap]
rs459718	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs460564	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4740833	1.00[CEU][hapmap];0.82[YRI][hapmap]
rs4742131	1.00[CEU][hapmap]
rs6477017	1.00[CEU][hapmap]
rs6477024	1.00[CEU][hapmap]
rs7019606	1.00[CEU][hapmap]
rs7021498	1.00[CEU][hapmap]
rs7024130	1.00[CEU][hapmap]
rs7026454	0.86[YRI][hapmap]
rs7029833	1.00[CEU][hapmap];0.88[YRI][hapmap]
rs7030731	1.00[CEU][hapmap]
rs7032130	1.00[CEU][hapmap];0.93[YRI][hapmap]
rs7034210	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs7042947	1.00[CEU][hapmap];0.86[JPT][hapmap];0.90[EUR][1000 genomes]
rs7044750	1.00[CEU][hapmap];0.92[YRI][hapmap]
rs7846916	0.80[CHB][hapmap];1.00[EUR][1000 genomes]
rs7866793	1.00[CEU][hapmap]
rs7868062	1.00[CEU][hapmap]
rs899381	0.90[EUR][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	nsv948847	chr9:5712626-6417677	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv1031086	chr9:5806949-6630686	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv539967	chr9:5806949-6630686	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	nsv892155	chr9:5825768-6044937	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv1015450	chr9:5915640-6114652	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:6020000-6023200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr9:6022400-6024000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr9:6023000-6024000	Weak transcription	HepG2	liver

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