Variant report

Variant	rs9476899
Chromosome Location	chr6:15725478-15725479
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:15718712..15722116-chr6:15722566..15727072,4	K562	blood:
2	chr6:15723984..15726678-chr6:15729144..15731299,3	MCF-7	breast:
3	chr6:15722743..15725547-chr6:16128093..16130865,2	K562	blood:
4	chr6:15711716..15714538-chr6:15724011..15725713,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DTNBP1-7	chr6:15725264-15726229	NONHSAT107877

Variant related genes	Relation type
ENSG00000007944	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1123073	1.00[ASN][1000 genomes]
rs17391774	1.00[ASN][1000 genomes]
rs17473838	1.00[CHD][hapmap]
rs17475195	1.00[CHD][hapmap]
rs2619536	1.00[ASN][1000 genomes]
rs2743851	1.00[ASN][1000 genomes]
rs2743852	1.00[ASN][1000 genomes]
rs2743873	1.00[ASN][1000 genomes]
rs2769561	1.00[ASN][1000 genomes]
rs2769562	1.00[ASN][1000 genomes]
rs2769563	1.00[ASN][1000 genomes]
rs2769567	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34765387	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs375310	1.00[CHD][hapmap]
rs62395006	1.00[ASN][1000 genomes]
rs62395016	1.00[ASN][1000 genomes]
rs62396141	1.00[ASN][1000 genomes]
rs62396142	1.00[ASN][1000 genomes]
rs62396148	1.00[ASN][1000 genomes]
rs62396775	1.00[ASN][1000 genomes]
rs6906528	1.00[CHD][hapmap]
rs6908299	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6913257	1.00[ASN][1000 genomes]
rs6937887	1.00[CHD][hapmap]
rs737072	0.84[YRI][hapmap]
rs742206	1.00[ASN][1000 genomes]
rs742207	1.00[ASN][1000 genomes]
rs742208	1.00[ASN][1000 genomes]
rs751529	0.81[YRI][hapmap]
rs7738190	1.00[CHD][hapmap]
rs7756793	1.00[ASN][1000 genomes]
rs7760793	1.00[CHD][hapmap]
rs9283925	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.81[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9296975	1.00[ASN][1000 genomes]
rs9464816	0.83[LWK][hapmap];1.00[ASN][1000 genomes]
rs9464817	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9464819	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9476890	1.00[ASN][1000 genomes]
rs9476894	1.00[ASN][1000 genomes]
rs9476895	0.84[YRI][hapmap]
rs9476897	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428136	chr6:15595640-15781241	Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	esv2755670	chr6:15624762-15736008	Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	esv2757157	chr6:15668867-15725478	Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	esv2759408	chr6:15668867-15725478	Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9476899	TBC1D7	cis	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:15721200-15736200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:15725200-15725800	Enhancers	K562	blood

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