Variant report

Variant	rs11582607
Chromosome Location	chr1:209989522-209989523
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:209969439..209971872-chr1:209988283..209991092,2	MCF-7	breast:
2	chr1:209986093..209989854-chr1:209998017..210002656,5	K562	blood:
3	chr1:209988063..209993866-chr1:209997170..210003138,6	MCF-7	breast:
4	chr1:209987591..209990855-chr1:209991529..209994207,3	K562	blood:

Variant related genes	Relation type
ENSG00000117597	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10127937	0.83[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10218448	0.84[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10489344	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11119344	0.84[CEU][hapmap]
rs11119354	1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.82[TSI][hapmap];0.84[ASN][1000 genomes]
rs11584081	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11590807	1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11810091	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12403006	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12404886	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17317580	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17389541	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2013196	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28601717	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34743335	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3753510	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3753513	0.83[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3766615	0.83[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs41274838	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4240837	0.83[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56071308	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56268268	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61820635	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6699507	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72741048	0.89[EUR][1000 genomes]
rs7526313	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7544804	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7546104	0.84[ASN][1000 genomes]
rs932334	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]

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	nsv999901	chr1:209600631-210205379	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv873139	chr1:209828955-210050794	Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11582607	IKBKE	cis	parietal	SCAN
rs11582607	IRF6	cis	cerebellum	SCAN
rs11582607	IRF6	cis	Whole Blood	GTEx
rs11582607	HHAT	cis	parietal	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209981800-209989600	Weak transcription	Spleen	Spleen
2	chr1:209981800-209989800	Weak transcription	Right Atrium	heart
3	chr1:209987800-209991200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:209988000-209991400	Enhancers	Fetal Thymus	thymus
5	chr1:209989000-209989600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr1:209989000-209990000	Flanking Active TSS	NHEK	skin
7	chr1:209989200-209989600	Enhancers	iPS-20b Cell Line	embryonic stem cell
8	chr1:209989200-209989600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr1:209989200-209989600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
10	chr1:209989200-209989600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr1:209989200-209989600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr1:209989200-209989600	Enhancers	GM12878-XiMat	blood
13	chr1:209989200-209989800	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr1:209989200-209989800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
15	chr1:209989200-209989800	Enhancers	Pancreas	Pancrea
16	chr1:209989200-209990000	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr1:209989200-209990000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
18	chr1:209989200-209990000	Enhancers	HepG2	liver
19	chr1:209989200-209990800	Enhancers	Placenta	Placenta
20	chr1:209989200-209991200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr1:209989200-209991200	Enhancers	Esophagus	oesophagus
22	chr1:209989400-209989600	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr1:209989400-209989600	Enhancers	HMEC	breast
24	chr1:209989400-209989800	Enhancers	H1 Cell Line	embryonic stem cell
25	chr1:209989400-209990000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr1:209989400-209990000	Enhancers	Fetal Muscle Trunk	muscle

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