Variant report

Variant	rs4308587
Chromosome Location	chr6:149440874-149440875
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:149425674..149427505-chr6:149439883..149441574,2	MCF-7	breast:
2	chr6:149440091..149442908-chr6:149453590..149455859,2	K562	blood:
3	chr6:149434484..149436638-chr6:149440096..149443619,3	MCF-7	breast:
4	chr6:149440205..149443227-chr6:149446390..149449238,3	K562	blood:
5	chr6:149438674..149441948-chr6:149450360..149452132,3	MCF-7	breast:

Extended variants
information (count: 31 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs12191264	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs12191441	0.80[CHB][hapmap];1.00[JPT][hapmap]
rs4357160	1.00[CEU][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];0.87[JPT][hapmap];0.89[MEX][hapmap];0.91[TSI][hapmap];0.94[EUR][1000 genomes]
rs4535574	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4895778	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55635503	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55843534	0.94[EUR][1000 genomes]
rs56052955	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56071715	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56098879	0.92[EUR][1000 genomes]
rs56227122	0.92[EUR][1000 genomes]
rs56367965	0.92[EUR][1000 genomes]
rs57116615	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58260766	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58500730	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60008694	0.85[EUR][1000 genomes]
rs60107332	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60424096	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61338555	0.92[EUR][1000 genomes]
rs61555942	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62425887	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62425895	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62425899	0.94[EUR][1000 genomes]
rs62425913	0.94[EUR][1000 genomes]
rs62425916	0.94[EUR][1000 genomes]
rs62425928	0.92[EUR][1000 genomes]
rs62428289	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9386246	0.87[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032319	chr6:149271433-149550525	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv538470	chr6:149271433-149550525	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv1024776	chr6:149398652-149654593	Weak transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4308587	SASH1	cis	cerebellum	SCAN
rs4308587	FBXO5	cis	parietal	SCAN
rs4308587	ALKBH6	trans	cerebellum	SCAN
rs4308587	AKAP12	cis	cerebellum	SCAN
rs4308587	RGS17	cis	parietal	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:149433200-149443400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
2	chr6:149433800-149444400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr6:149436400-149442600	Enhancers	Primary hematopoietic stem cells	blood
4	chr6:149437400-149444400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr6:149439600-149441400	Enhancers	Primary hematopoietic stem cells short term culture	blood
6	chr6:149440000-149441000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr6:149440200-149441000	Enhancers	Muscle Satellite Cultured Cells	--
8	chr6:149440400-149443000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr6:149440600-149442400	Enhancers	K562	blood
10	chr6:149440600-149443200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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