Variant report

Variant	rs12026940
Chromosome Location	chr1:221945714-221945715
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:221943490..221945963-chr1:221951979..221954121,2	MCF-7	breast:

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10495178	0.88[CEU][hapmap];0.95[CHB][hapmap];0.81[CHD][hapmap];0.92[GIH][hapmap];0.93[JPT][hapmap];0.83[EUR][1000 genomes]
rs11118858	0.90[CHB][hapmap];0.91[CHD][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs12022218	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12030246	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12034339	0.81[EUR][1000 genomes]
rs12036282	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.96[GIH][hapmap];0.93[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12038356	0.81[EUR][1000 genomes]
rs12039269	0.81[EUR][1000 genomes]
rs12041329	0.81[EUR][1000 genomes]
rs17010785	0.81[EUR][1000 genomes]
rs3003901	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58234964	0.83[EUR][1000 genomes]
rs58787358	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6680297	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6680316	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6680505	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6680586	0.81[ASN][1000 genomes]
rs72629678	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7532339	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.90[YRI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9441946	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469786	chr1:221855871-222040335	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv482867	chr1:221855871-222040335	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1002463	chr1:221863355-222095773	Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv535302	chr1:221863355-222095773	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv1007092	chr1:221883491-221958279	Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
6	nsv535303	chr1:221883491-221958279	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12026940		cis	Lymphoblastoid	GTEx
rs12026940	hmm26268	cis	multi-tissue	Pritchard

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:221942800-221947400	Weak transcription	HUVEC	blood vessel
2	chr1:221944600-221947400	Enhancers	Hela-S3	cervix
3	chr1:221945000-221946400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr1:221945000-221946400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr1:221945200-221946000	Enhancers	Muscle Satellite Cultured Cells	--
6	chr1:221945200-221946400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr1:221945200-221946400	Enhancers	GM12878-XiMat	blood
8	chr1:221945400-221949600	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr1:221945600-221946000	Enhancers	HSMMtube	muscle

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