Variant report

Variant	rs9296260
Chromosome Location	chr6:38692437-38692438
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	chr6:38670885..38672648-chr6:38689794..38692471,2	K562	blood:
2	chr6:38669241..38671536-chr6:38691000..38694946,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000124767	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1018420	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs1033524	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs12196388	1.00[CHB][hapmap]
rs12208880	1.00[CHB][hapmap]
rs12209872	1.00[CHB][hapmap]
rs13196250	1.00[CHB][hapmap]
rs13208143	1.00[CHB][hapmap]
rs13213448	1.00[CHB][hapmap]
rs13219077	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs1625177	1.00[CHB][hapmap]
rs1631117	1.00[CHD][hapmap]
rs1698998	0.85[LWK][hapmap];0.91[MKK][hapmap];0.83[YRI][hapmap]
rs17620389	1.00[CHD][hapmap]
rs1781723	1.00[CHB][hapmap]
rs1937777	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs6923304	1.00[CHB][hapmap]
rs6928323	1.00[CHB][hapmap]
rs6930268	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs7742625	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs7761815	0.95[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021991	chr6:37893949-38738720	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	esv2758049	chr6:38588969-38711085	Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	esv2759421	chr6:38588969-38711085	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv427754	chr6:38588969-38711085	Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	nsv428144	chr6:38588969-38711085	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
7	nsv830642	chr6:38645056-38800657	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9296260	C6orf222	cis	parietal	SCAN
rs9296260	FANCE	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38688600-38693200	Weak transcription	HUVEC	blood vessel
2	chr6:38692400-38693400	Genic enhancers	K562	blood

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