Variant report

Variant	rs471539
Chromosome Location	chr11:73971193-73971194
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:73970088..73972643-chr11:73975001..73976795,2	MCF-7	breast:

Extended variants
information (count: 31 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11236006	0.87[CEU][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.81[TSI][hapmap];0.80[YRI][hapmap]
rs11236008	0.82[ASW][hapmap];0.87[CEU][hapmap];0.90[CHB][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.96[LWK][hapmap];0.89[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap]
rs11236028	0.84[CEU][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];0.86[JPT][hapmap];0.81[MEX][hapmap]
rs11825568	0.86[JPT][hapmap]
rs1279116	0.81[ASN][1000 genomes]
rs1941820	0.90[CHB][hapmap];0.87[CHD][hapmap];0.81[GIH][hapmap];0.87[JPT][hapmap]
rs2848557	0.84[CEU][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];0.93[JPT][hapmap]
rs3018185	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4522190	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs475326	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4944880	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs530699	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs542628	0.90[CHB][hapmap];0.87[CHD][hapmap];0.83[GIH][hapmap];0.87[JPT][hapmap]
rs544356	0.90[CHB][hapmap]
rs555964	0.84[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.93[JPT][hapmap]
rs562488	0.90[CHB][hapmap];0.87[JPT][hapmap]
rs699142	0.89[CHB][hapmap]
rs72984885	0.92[AFR][1000 genomes]
rs72984886	0.92[AFR][1000 genomes]
rs7925988	0.87[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap]
rs7930356	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs826054	0.90[CHB][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap]
rs826057	0.90[CHB][hapmap];0.87[CHD][hapmap]
rs826058	0.90[CHB][hapmap];0.87[CHD][hapmap]
rs866650	0.80[CHB][hapmap];0.85[JPT][hapmap]
rs869616	0.87[CEU][hapmap];0.80[CHB][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.84[TSI][hapmap];0.80[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757451	chr11:73842609-74545888	Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	esv2759837	chr11:73842609-74557597	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	esv34979	chr11:73878688-74533452	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
4	esv2758277	chr11:73887567-74557597	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
5	nsv825994	chr11:73936667-74534455	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs471539	CCDC27	trans	cerebellum	SCAN
rs471539	C2CD3	cis	parietal	SCAN
rs471539	PPME1	cis	cerebellum	SCAN
rs471539	MRPL48	cis	cerebellum	SCAN
rs471539	UCP2	Cis_1M	lymphoblastoid	RTeQTL
rs471539	RSF1	cis	parietal	SCAN
rs471539	PGM2L1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:73966000-73971800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr11:73966000-73972000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr11:73966200-73971400	Weak transcription	NHEK	skin
4	chr11:73966200-73980000	Weak transcription	Gastric	stomach
5	chr11:73966400-73979200	Weak transcription	Primary T cells from cord blood	blood
6	chr11:73966600-73972000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr11:73967000-73971800	Weak transcription	Liver	Liver
8	chr11:73968000-73971200	Weak transcription	Fetal Muscle Trunk	muscle
9	chr11:73968000-73979000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr11:73968200-73973600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr11:73968400-73971200	Enhancers	Skeletal Muscle Female	skeletal muscle
12	chr11:73968400-73971400	Enhancers	Skeletal Muscle Male	skeletal muscle
13	chr11:73969400-73987600	Weak transcription	NH-A	brain
14	chr11:73969600-73971400	Genic enhancers	A549	lung
15	chr11:73969600-73972400	Enhancers	Placenta	Placenta
16	chr11:73969600-73974200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr11:73969800-73971200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr11:73969800-73971200	Weak transcription	Fetal Muscle Leg	muscle
19	chr11:73969800-73978200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr11:73969800-73980400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr11:73970000-73980000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr11:73970000-73987600	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr11:73970200-73971200	Weak transcription	Psoas Muscle	Psoas
24	chr11:73970200-73972000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr11:73970600-73978000	Weak transcription	Hela-S3	cervix
26	chr11:73971000-73971400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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