Variant report

Variant	rs11072509
Chromosome Location	chr15:75114374-75114375
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:75074174..75075858-chr15:75112738..75114767,2	MCF-7	breast:
2	chr15:75074461..75076806-chr15:75112062..75114585,2	K562	blood:
3	chr15:75113859..75115829-chr15:75135120..75137203,2	MCF-7	breast:
4	chr15:75112517..75114870-chr15:75115640..75117170,2	MCF-7	breast:
5	chr15:75113543..75115731-chr15:75122217..75124290,2	K562	blood:
6	chr15:75108017..75109912-chr15:75114230..75116710,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000140506	Chromatin interaction
ENSG00000261606	Chromatin interaction
ENSG00000103653	Chromatin interaction
ENSG00000140474	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11634474	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12441505	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12442901	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1350193	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1378938	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2071501	0.87[ASN][1000 genomes]
rs2168519	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2301249	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3784790	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3935077	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4886615	0.82[EUR][1000 genomes]
rs4886619	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4886629	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7085	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7162232	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7176022	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7180484	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72625792	0.84[ASN][1000 genomes]
rs72730503	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8033381	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs936226	0.85[EUR][1000 genomes]
rs936228	0.81[EUR][1000 genomes]
rs936229	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904380	chr15:74869438-75142761	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
2	nsv833055	chr15:74988344-75166288	Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv520527	chr15:75108636-75122856	Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv904381	chr15:75108636-75242155	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11072509	MPI	Cis_1M	lymphoblastoid	RTeQTL
rs11072509	COX5A	Cis_1M	lymphoblastoid	RTeQTL
rs11072509	ULK3	cis	Whole Blood	GTEx

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75107200-75114400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr15:75109800-75116800	Weak transcription	Brain Anterior Caudate	brain
3	chr15:75110800-75115000	Enhancers	Primary B cells from peripheral blood	blood
4	chr15:75111400-75128000	Weak transcription	Gastric	stomach
5	chr15:75112400-75114400	Enhancers	Primary B cells from cord blood	blood
6	chr15:75112400-75114800	Enhancers	Fetal Brain Male	brain
7	chr15:75112600-75114400	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr15:75112800-75114400	Enhancers	GM12878-XiMat	blood
9	chr15:75113000-75114400	Enhancers	HUES6 Cell Line	embryonic stem cell
10	chr15:75113000-75114400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr15:75113000-75115000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr15:75113200-75114400	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr15:75113200-75114400	Enhancers	H1 Cell Line	embryonic stem cell
14	chr15:75113200-75114400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
15	chr15:75113200-75114400	Enhancers	Hela-S3	cervix
16	chr15:75113400-75114600	Enhancers	Spleen	Spleen
17	chr15:75113600-75114400	Enhancers	iPS-20b Cell Line	embryonic stem cell
18	chr15:75113600-75118600	Weak transcription	Right Atrium	heart
19	chr15:75113800-75114400	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr15:75113800-75115200	Weak transcription	Duodenum Mucosa	Duodenum
21	chr15:75114000-75114800	Enhancers	Fetal Brain Female	brain
22	chr15:75114000-75115000	Enhancers	Brain Germinal Matrix	brain
23	chr15:75114200-75114400	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin

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