Variant report

Variant	rs2744257
Chromosome Location	chr6:25267748-25267749
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:25266060..25267780-chr6:26028723..26030730,2	K562	blood:
2	chr6:25265692..25268532-chr6:25269921..25272055,2	MCF-7	breast:
3	chr6:25265953..25268779-chr6:25278296..25280757,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000079691	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs1016855	0.91[CEU][hapmap];0.90[CHD][hapmap];0.85[GIH][hapmap];0.87[ASN][1000 genomes]
rs2690054	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.96[CHD][hapmap];0.85[GIH][hapmap];0.85[MEX][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2690061	0.86[EUR][1000 genomes]
rs2690064	0.95[CEU][hapmap];0.88[CHB][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2690067	0.87[CEU][hapmap];0.85[EUR][1000 genomes]
rs2690074	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs2744254	0.87[CEU][hapmap];0.85[EUR][1000 genomes]
rs2744258	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744267	1.00[CEU][hapmap];0.84[TSI][hapmap];0.89[EUR][1000 genomes]
rs2744268	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs2744269	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6908902	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6909014	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6914799	0.91[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];0.87[ASN][1000 genomes]
rs6926126	0.91[CEU][hapmap];0.80[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];0.87[ASN][1000 genomes]
rs721037	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs723048	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9358848	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9358849	0.83[CEU][hapmap]
rs9393635	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][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	nsv1023989	chr6:24930362-25285679	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv1025694	chr6:25136860-25309450	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv1020774	chr6:25154152-25285679	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv538161	chr6:25154152-25285679	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv883483	chr6:25200842-25272435	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv883484	chr6:25237288-25303100	Active TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv883485	chr6:25259137-25437986	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv883486	chr6:25260434-25422369	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2744257	HIST1H3G	cis	parietal	SCAN
rs2744257	PIP	trans	cerebellum	SCAN
rs2744257	HIST1H4L	cis	cerebellum	SCAN
rs2744257	SLC17A1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25267400-25268000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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