Variant report

Variant	rs11227306
Chromosome Location	chr11:65578672-65578673
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:65572431..65575992-chr11:65577073..65580211,5	MCF-7	breast:
2	chr11:65547646..65551396-chr11:65574848..65579381,6	K562	blood:
3	chr11:65577404..65580770-chr11:65592566..65594874,3	K562	blood:
4	chr11:65572404..65575326-chr11:65576083..65580070,3	K562	blood:
5	chr11:65577781..65579327-chr11:65656860..65658905,2	K562	blood:
6	chr11:65575640..65578882-chr11:65620145..65623092,3	K562	blood:
7	chr11:65576308..65578705-chr11:65600271..65604336,3	MCF-7	breast:
8	chr11:65578671..65581535-chr11:65584408..65587256,5	K562	blood:
9	chr11:65483666..65485894-chr11:65578594..65581279,2	MCF-7	breast:
10	chr11:65577980..65580904-chr11:65655568..65657932,2	K562	blood:
11	chr11:65428811..65431041-chr11:65577334..65579546,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000175602	Chromatin interaction
ENSG00000172500	Chromatin interaction
ENSG00000173039	Chromatin interaction
ENSG00000172977	Chromatin interaction
ENSG00000172803	Chromatin interaction
ENSG00000254470	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10896056	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11227310	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11227313	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11227314	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11227315	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12800497	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2303385	0.92[CEU][hapmap];0.91[MEX][hapmap]
rs35138525	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7102454	0.82[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.81[YRI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7928652	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7940691	0.92[CEU][hapmap];0.91[MEX][hapmap]

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	nsv897736	chr11:65335705-65676516	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	227 gene(s)	inside rSNPs	diseases
2	nsv430401	chr11:65419324-65788024	Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	224 gene(s)	inside rSNPs	diseases
3	esv2758274	chr11:65559893-65722363	Genic enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
4	esv2759834	chr11:65559893-65722363	Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
5	nsv427890	chr11:65559893-65722363	Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
6	esv10330	chr11:65573764-65580076	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	esv2762915	chr11:65575850-65580638	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
8	esv3357995	chr11:65575876-65580074	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers	Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
DNA methylation (variation)	23725790	GWAS catalog

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs11227306	CTSW	cis	Whole Blood	GTEx
rs11227306	RBM4	cis	cerebellum	SCAN
rs11227306	CTSW	cis	lung	GTEx
rs11227306	SNX32	cis	cerebellum	SCAN
rs11227306	LRRN4CL	cis	cerebellum	SCAN
rs11227306	EIF1AD	cis	parietal	SCAN
rs11227306	SNX32	cis	parietal	SCAN
rs11227306	PCNXL3	cis	parietal	SCAN
rs11227306	FRMD8	cis	parietal	SCAN
rs11227306	TPCN2	cis	cerebellum	SCAN
rs11227306	EFEMP2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65574600-65581400	Weak transcription	Fetal Intestine Small	intestine
2	chr11:65575000-65580000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr11:65575400-65583800	Weak transcription	Brain Substantia Nigra	brain
4	chr11:65576400-65586000	Weak transcription	Spleen	Spleen
5	chr11:65577400-65581200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr11:65577600-65578800	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
7	chr11:65577600-65579600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr11:65577800-65583200	Enhancers	Adipose Nuclei	Adipose
9	chr11:65577800-65584400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr11:65578000-65578800	Enhancers	Lung	lung
11	chr11:65578000-65582200	Weak transcription	Left Ventricle	heart
12	chr11:65578000-65584800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr11:65578200-65579200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr11:65578200-65581600	Weak transcription	Pancreas	Pancrea
15	chr11:65578200-65582400	Weak transcription	Esophagus	oesophagus
16	chr11:65578200-65584400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr11:65578200-65585200	Weak transcription	Right Ventricle	heart
18	chr11:65578200-65585400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr11:65578200-65585400	Weak transcription	Gastric	stomach
20	chr11:65578400-65582000	Enhancers	Primary neutrophils fromperipheralblood	blood
21	chr11:65578600-65578800	Bivalent Enhancer	Duodenum Mucosa	Duodenum
22	chr11:65578600-65579400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr11:65578600-65585000	Enhancers	Placenta	Placenta

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