Variant report

Variant	rs826054
Chromosome Location	chr11:73800001-73800002
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:73780866..73784002-chr11:73798180..73802078,6	MCF-7	breast:
2	chr11:73798903..73800889-chr11:73801297..73804030,2	K562	blood:
3	chr11:73798926..73801362-chr11:73893492..73896056,2	K562	blood:
4	chr11:73778180..73781840-chr11:73797440..73801034,4	MCF-7	breast:
5	chr11:73791960..73793657-chr11:73799383..73800978,2	MCF-7	breast:
6	chr11:73695027..73697891-chr11:73799212..73800903,2	K562	blood:

Variant related genes	Relation type
ENSG00000168014	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs11236004	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11236006	0.83[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.90[ASN][1000 genomes]
rs11236008	0.83[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.91[ASN][1000 genomes]
rs11236028	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.84[ASN][1000 genomes]
rs11825568	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11825974	0.94[ASN][1000 genomes]
rs15763	0.83[CHD][hapmap];0.93[JPT][hapmap]
rs1626521	0.83[CEU][hapmap];0.83[CHD][hapmap];0.93[JPT][hapmap]
rs1685354	0.93[JPT][hapmap]
rs1790400	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2632723	0.93[JPT][hapmap]
rs2734827	0.84[CHD][hapmap];0.93[JPT][hapmap]
rs2848557	0.88[CEU][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];0.93[JPT][hapmap];0.92[TSI][hapmap]
rs4944880	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs530699	0.90[CHB][hapmap];0.93[JPT][hapmap]
rs555964	0.88[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];0.93[JPT][hapmap];0.92[TSI][hapmap]
rs562488	0.81[CHB][hapmap]
rs60647229	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs668514	0.93[JPT][hapmap]
rs699142	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72984831	0.88[ASN][1000 genomes]
rs72984885	0.84[ASN][1000 genomes]
rs72984886	0.84[ASN][1000 genomes]
rs7925988	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs826055	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs826057	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.92[TSI][hapmap];0.89[YRI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs826058	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.90[TSI][hapmap];0.89[YRI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs866650	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs869616	0.83[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.84[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv492091	chr11:73285970-73844424	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs826054	PPME1	cis	cerebellum	SCAN
rs826054	C2CD3	cis	parietal	SCAN
rs826054	UCP2	cis	multi-tissue	Pritchard
rs826054	MRPL48	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:73730800-73800800	Weak transcription	Fetal Heart	heart
2	chr11:73750800-73800400	Weak transcription	HMEC	breast
3	chr11:73753200-73804600	Weak transcription	Colonic Mucosa	Colon
4	chr11:73760000-73802600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr11:73777600-73818600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr11:73781800-73849200	Weak transcription	Stomach Mucosa	stomach
7	chr11:73782600-73823800	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr11:73784200-73801000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr11:73785400-73800400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr11:73785600-73800200	Weak transcription	NH-A	brain
11	chr11:73785600-73803400	Weak transcription	NHDF-Ad	bronchial
12	chr11:73785600-73823600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr11:73787800-73811400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr11:73789400-73800800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr11:73789600-73800600	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr11:73789800-73800600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr11:73789800-73800600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr11:73789800-73801000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr11:73790000-73800600	Weak transcription	Esophagus	oesophagus
20	chr11:73790200-73800400	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr11:73793800-73800600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr11:73794600-73823600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr11:73794800-73800600	Strong transcription	Fetal Thymus	thymus
24	chr11:73794800-73804200	Strong transcription	Brain Angular Gyrus	brain
25	chr11:73794800-73805400	Strong transcription	Cortex derived primary cultured neurospheres	brain
26	chr11:73794800-73806600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr11:73794800-73806600	Strong transcription	Fetal Lung	lung
28	chr11:73795000-73806000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr11:73795000-73806000	Strong transcription	Brain Anterior Caudate	brain
30	chr11:73795000-73806400	Strong transcription	Adipose Nuclei	Adipose
31	chr11:73795000-73806600	Strong transcription	Fetal Muscle Leg	muscle
32	chr11:73795000-73808600	Strong transcription	HUES64 Cell Line	embryonic stem cell
33	chr11:73795000-73817400	Strong transcription	Primary neutrophils fromperipheralblood	blood
34	chr11:73795000-73817600	Strong transcription	Primary B cells from cord blood	blood
35	chr11:73795200-73800800	Strong transcription	Dnd41	blood
36	chr11:73795200-73802400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr11:73795200-73805000	Strong transcription	HUES6 Cell Line	embryonic stem cell
38	chr11:73795200-73805800	Strong transcription	Duodenum Mucosa	Duodenum
39	chr11:73795200-73806000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr11:73795200-73806000	Strong transcription	Placenta	Placenta
41	chr11:73795200-73806400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
42	chr11:73795200-73806400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
43	chr11:73795200-73806400	Strong transcription	HSMMtube	muscle
44	chr11:73795200-73806600	Strong transcription	HUES48 Cell Line	embryonic stem cell
45	chr11:73795200-73807200	Strong transcription	Rectal Mucosa Donor 29	rectum
46	chr11:73795200-73814600	Strong transcription	Fetal Muscle Trunk	muscle
47	chr11:73795200-73814600	Strong transcription	Left Ventricle	heart
48	chr11:73795200-73814800	Strong transcription	Liver	Liver
49	chr11:73795200-73815200	Strong transcription	Rectal Mucosa Donor 31	rectum
50	chr11:73795200-73817600	Strong transcription	Primary T cells from cord blood	blood

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