Variant report

Variant	rs10896053
Chromosome Location	chr11:65579670-65579671
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:65572431..65575992-chr11:65577073..65580211,5	MCF-7	breast:
2	chr11:65577404..65580770-chr11:65592566..65594874,3	K562	blood:
3	chr11:65572404..65575326-chr11:65576083..65580070,3	K562	blood:
4	chr11:65578671..65581535-chr11:65584408..65587256,5	K562	blood:
5	chr11:65483666..65485894-chr11:65578594..65581279,2	MCF-7	breast:
6	chr11:65577980..65580904-chr11:65655568..65657932,2	K562	blood:

Variant related genes	Relation type
ENSG00000172977	Chromatin interaction
ENSG00000175602	Chromatin interaction
ENSG00000172500	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10791825	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10791826	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10791828	0.82[JPT][hapmap]
rs10896049	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10896055	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1151515	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1204771	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1204772	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.92[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12420336	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13817	0.88[GIH][hapmap]
rs1939212	0.85[GIH][hapmap]
rs4930162	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4930322	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4930325	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs521004	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs550976	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs558114	0.88[GIH][hapmap]
rs56169730	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58836187	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs601887	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.92[TSI][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60678003	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61895685	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs621348	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs630303	0.88[GIH][hapmap]
rs635375	0.88[GIH][hapmap]
rs646675	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs648732	0.88[GIH][hapmap]
rs652021	0.88[GIH][hapmap]
rs656040	0.88[GIH][hapmap]
rs6591191	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs659857	0.88[GIH][hapmap]
rs665306	0.88[GIH][hapmap]
rs668356	0.88[GIH][hapmap]
rs7112754	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7113768	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7114014	0.84[GIH][hapmap]
rs7114237	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72924752	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9971612	0.82[AMR][1000 genomes]

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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10896053	MACROD1	cis	parietal	SCAN
rs10896053	GPHA2	cis	parietal	SCAN
rs10896053	EFEMP2	cis	multi-tissue	Pritchard
rs10896053	ANKRD13D	cis	parietal	SCAN
rs10896053	CARNS1	cis	cerebellum	SCAN

Chromatin state (count:30 , 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	chr11:65577800-65583200	Enhancers	Adipose Nuclei	Adipose
7	chr11:65577800-65584400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr11:65578000-65582200	Weak transcription	Left Ventricle	heart
9	chr11:65578000-65584800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr11:65578200-65581600	Weak transcription	Pancreas	Pancrea
11	chr11:65578200-65582400	Weak transcription	Esophagus	oesophagus
12	chr11:65578200-65584400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr11:65578200-65585200	Weak transcription	Right Ventricle	heart
14	chr11:65578200-65585400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr11:65578200-65585400	Weak transcription	Gastric	stomach
16	chr11:65578400-65582000	Enhancers	Primary neutrophils fromperipheralblood	blood
17	chr11:65578600-65585000	Enhancers	Placenta	Placenta
18	chr11:65578800-65584400	Weak transcription	Lung	lung
19	chr11:65579200-65580000	Enhancers	HSMMtube	muscle
20	chr11:65579200-65584400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr11:65579400-65579800	Bivalent Enhancer	Fetal Muscle Leg	muscle
22	chr11:65579400-65579800	Enhancers	Placenta Amnion	Placenta Amnion
23	chr11:65579400-65579800	Bivalent Enhancer	NHDF-Ad	bronchial
24	chr11:65579400-65580000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
25	chr11:65579400-65581800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr11:65579400-65585000	Weak transcription	Primary T cells from cord blood	blood
27	chr11:65579600-65579800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr11:65579600-65579800	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr11:65579600-65579800	Enhancers	Stomach Smooth Muscle	stomach
30	chr11:65579600-65585200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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