Variant report

Variant	rs555964
Chromosome Location	chr11:73906924-73906925
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:73899140..73901160-chr11:73903960..73907119,3	K562	blood:
2	chr11:73902734..73904600-chr11:73906039..73908502,2	K562	blood:

Extended variants
information (count: 36 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11236004	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11236006	0.90[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs11236008	0.90[CHB][hapmap];0.88[CHD][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs11236028	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11825568	0.87[CEU][hapmap];0.93[JPT][hapmap];0.80[EUR][1000 genomes]
rs1291934	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs15763	0.93[JPT][hapmap]
rs1626521	0.93[JPT][hapmap]
rs1685354	0.93[JPT][hapmap]
rs1941820	0.90[CHB][hapmap]
rs2632723	0.93[JPT][hapmap]
rs2734827	0.93[JPT][hapmap]
rs2848557	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3018185	0.94[ASN][1000 genomes]
rs4522190	0.83[ASN][1000 genomes]
rs4944880	0.88[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];0.81[EUR][1000 genomes]
rs530699	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs542628	0.90[CHB][hapmap]
rs544356	0.90[CHB][hapmap];0.81[CHD][hapmap]
rs562488	0.90[CHB][hapmap]
rs58006161	0.89[ASN][1000 genomes]
rs60647229	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs699142	0.88[CEU][hapmap];0.89[CHB][hapmap]
rs72984885	0.94[ASN][1000 genomes]
rs72984886	0.94[ASN][1000 genomes]
rs7925988	0.90[CHB][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs826054	0.88[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];0.93[JPT][hapmap];0.92[TSI][hapmap]
rs826057	0.88[CEU][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];0.90[TSI][hapmap]
rs826058	0.88[CEU][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];0.85[GIH][hapmap];0.88[TSI][hapmap]
rs866650	0.87[CEU][hapmap];0.93[JPT][hapmap]
rs869616	0.90[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];0.94[ASN][1000 genomes]

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	nsv522994	chr11:73906924-73917190	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs555964	PGM2L1	cis	parietal	SCAN
rs555964	UCP2	cis	multi-tissue	Pritchard
rs555964	PPME1	cis	cerebellum	SCAN
rs555964	C2CD3	cis	parietal	SCAN
rs555964	UCP2	Cis_1M	lymphoblastoid	RTeQTL
rs555964	MRPL48	cis	cerebellum	SCAN

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:73883600-73915000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr11:73883600-73915200	Weak transcription	Fetal Muscle Trunk	muscle
3	chr11:73883600-73921000	Weak transcription	Esophagus	oesophagus
4	chr11:73883600-73923200	Weak transcription	Aorta	Aorta
5	chr11:73883800-73915000	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr11:73883800-73920000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr11:73883800-73923200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr11:73884200-73907000	Weak transcription	Fetal Lung	lung
9	chr11:73884200-73915000	Weak transcription	Brain Anterior Caudate	brain
10	chr11:73884200-73915200	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr11:73884200-73915400	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr11:73884200-73916200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr11:73884200-73917600	Weak transcription	Ovary	ovary
14	chr11:73884200-73920200	Weak transcription	Thymus	Thymus
15	chr11:73884200-73941200	Weak transcription	Rectal Smooth Muscle	rectum
16	chr11:73884200-73941800	Weak transcription	Small Intestine	intestine
17	chr11:73884400-73915200	Weak transcription	Liver	Liver
18	chr11:73884400-73915200	Weak transcription	Duodenum Mucosa	Duodenum
19	chr11:73885600-73920200	Weak transcription	Colon Smooth Muscle	Colon
20	chr11:73885600-73920600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr11:73885600-73925600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr11:73885600-73957000	Weak transcription	Fetal Brain Male	brain
23	chr11:73885800-73942400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr11:73888400-73909600	Weak transcription	Right Atrium	heart
25	chr11:73891200-73915200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr11:73891200-73920200	Weak transcription	Brain Angular Gyrus	brain
27	chr11:73891400-73918400	Weak transcription	Osteobl	bone
28	chr11:73891400-73919800	Weak transcription	Brain Cingulate Gyrus	brain
29	chr11:73891400-73924000	Weak transcription	Brain Hippocampus Middle	brain
30	chr11:73893800-73908600	Weak transcription	Placenta	Placenta
31	chr11:73894000-73921600	Weak transcription	Pancreas	Pancrea
32	chr11:73894400-73915000	Weak transcription	Left Ventricle	heart
33	chr11:73895800-73915400	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr11:73897200-73915000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr11:73897200-73918800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr11:73897200-73937600	Weak transcription	Fetal Heart	heart
37	chr11:73897600-73923200	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr11:73897600-73923400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr11:73899600-73915200	Weak transcription	Fetal Thymus	thymus
40	chr11:73900000-73914800	Weak transcription	Hela-S3	cervix
41	chr11:73901000-73920200	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr11:73901400-73915800	Weak transcription	HepG2	liver
43	chr11:73901600-73915400	Weak transcription	Primary hematopoietic stem cells	blood
44	chr11:73901600-73938000	Weak transcription	Psoas Muscle	Psoas
45	chr11:73901800-73915000	Weak transcription	Fetal Intestine Large	intestine
46	chr11:73901800-73915200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr11:73902200-73916400	Weak transcription	Stomach Smooth Muscle	stomach
48	chr11:73902200-73936200	Weak transcription	Primary T cells fromperipheralblood	blood
49	chr11:73902400-73907000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr11:73902400-73914800	Weak transcription	HUES48 Cell Line	embryonic stem cell

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