Variant report

Variant	rs3957366
Chromosome Location	chr6:56905274-56905275
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:56877566..56879114-chr6:56904825..56906566,2	MCF-7	breast:
2	chr6:56834918..56837868-chr6:56903962..56906582,2	MCF-7	breast:
3	chr6:56903865..56905391-chr6:56992094..56994169,2	K562	blood:
4	chr6:56820096..56821611-chr6:56902889..56905830,2	K562	blood:
5	chr6:56818651..56821611-chr6:56903596..56905830,2	K562	blood:
6	chr6:56890706..56893193-chr6:56903389..56905342,2	K562	blood:
7	chr6:56900127..56902056-chr6:56904004..56905904,2	K562	blood:

Variant related genes	Relation type
ENSG00000151914	Chromatin interaction
ENSG00000151917	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1044670	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];0.81[TSI][hapmap];0.91[AFR][1000 genomes]
rs10456192	0.84[EUR][1000 genomes]
rs10484410	0.88[CEU][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes]
rs12190575	0.86[EUR][1000 genomes]
rs12192222	0.85[EUR][1000 genomes]
rs12194407	0.84[EUR][1000 genomes]
rs12198801	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12201039	0.90[AFR][1000 genomes]
rs12214119	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12214882	0.88[CEU][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13207768	1.00[ASW][hapmap]
rs1599280	1.00[ASW][hapmap]
rs17619360	0.88[CEU][hapmap];0.85[MEX][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes]
rs17685277	1.00[ASW][hapmap]
rs3800023	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs41267681	0.91[AFR][1000 genomes]
rs6459178	0.88[CEU][hapmap];0.85[MEX][hapmap];0.92[TSI][hapmap];0.85[EUR][1000 genomes]
rs6918222	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6936506	0.82[EUR][1000 genomes]
rs6936560	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs720884	1.00[ASW][hapmap]
rs7753927	0.83[TSI][hapmap]
rs7756421	0.88[CEU][hapmap];0.85[MEX][hapmap];0.92[TSI][hapmap]
rs7771115	0.88[CEU][hapmap];0.85[MEX][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491933	chr6:56177722-57171010	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv934026	chr6:56382056-57184218	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv533050	chr6:56504480-57297586	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv1021651	chr6:56569444-56966319	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv538228	chr6:56569444-56966319	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	esv3430228	chr6:56830972-57079281	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv1026524	chr6:56902544-56951703	Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
8	nsv970717	chr6:56903957-56955783	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs3957366	KIAA1586	Cis_1M	lymphoblastoid	RTeQTL
rs3957366	RAB23	cis	multi-tissue	Pritchard
rs3957366	RAB23	Cis_1M	lymphoblastoid	RTeQTL
rs3957366	BEND6	cis	parietal	SCAN
rs3957366	BEND6	cis	cerebellum	SCAN
rs3957366	BEND6	cis	Muscle Skeletal	GTEx
rs3957366	HMGCLL1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56878600-56905400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr6:56905000-56906000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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