Variant report

Variant	rs2554012
Chromosome Location	chr11:36395345-36395346
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr11:36395224-36395557	K562	blood:	n/a	chr11:36395368-36395379
2	CEBPB	chr11:36395200-36395553	HepG2	liver:	n/a	chr11:36395368-36395379
3	FOXP2	chr11:36395298-36395489	SK-N-MC	brain:	n/a	n/a
4	CEBPB	chr11:36395198-36395551	IMR90	lung:	n/a	chr11:36395368-36395379
5	POLR2A	chr11:36395041-36395846	SK-N-MC	brain:	n/a	n/a
6	CEBPB	chr11:36395161-36395615	A549	lung:	n/a	chr11:36395368-36395379
7	CEBPB	chr11:36395191-36395563	A549	lung:	n/a	chr11:36395368-36395379
8	CEBPB	chr11:36395198-36395567	K562	blood:	n/a	chr11:36395368-36395379
9	CEBPB	chr11:36395233-36395482	Hela-S3	cervix:	n/a	chr11:36395368-36395379
10	CEBPB	chr11:36395255-36395565	A549	lung:	n/a	chr11:36395368-36395379
11	CEBPB	chr11:36395242-36395418	K562	blood:	n/a	chr11:36395368-36395379

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:36393103..36395662-chr11:36402907..36405828,2	MCF-7	breast:
2	chr11:36331050..36333326-chr11:36394222..36396312,2	MCF-7	breast:

Variant related genes	Relation type
PRR5L	TF binding region

Extended variants
information (count: 8 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11033575	0.81[JPT][hapmap]
rs11033576	1.00[ASN][1000 genomes]
rs1816923	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4756307	0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs525634	0.91[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.97[ASN][1000 genomes]
rs7115677	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv467791	chr11:36108497-36999385	Flanking Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv554003	chr11:36108497-36999385	ZNF genes & repeats Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2554012	COMMD9	cis	parietal	SCAN
rs2554012	CD59	cis	cerebellum	SCAN
rs2554012	DEPDC7	cis	parietal	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:36388000-36397200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr11:36388600-36397000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr11:36389600-36397600	Weak transcription	Spleen	Spleen
4	chr11:36391600-36397400	Enhancers	Fetal Intestine Large	intestine
5	chr11:36392200-36397400	Enhancers	Fetal Intestine Small	intestine
6	chr11:36392800-36395600	Enhancers	Duodenum Mucosa	Duodenum
7	chr11:36393600-36395600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr11:36393800-36395400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr11:36393800-36395600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr11:36393800-36397200	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr11:36394000-36395600	Enhancers	Adipose Nuclei	Adipose
12	chr11:36394200-36397400	Weak transcription	Colonic Mucosa	Colon
13	chr11:36394200-36397600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr11:36394200-36397600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr11:36394400-36395600	Enhancers	Osteobl	bone
16	chr11:36394400-36396400	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr11:36394400-36396800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr11:36394400-36397000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr11:36394400-36397400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr11:36394400-36397400	Weak transcription	Ovary	ovary
21	chr11:36394400-36397400	Weak transcription	HMEC	breast
22	chr11:36394400-36397600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr11:36394400-36397800	Weak transcription	Gastric	stomach
24	chr11:36394600-36396800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr11:36394600-36396800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr11:36394600-36397200	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr11:36394600-36397400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr11:36394600-36397400	Weak transcription	Hela-S3	cervix
29	chr11:36394600-36397600	Weak transcription	Stomach Mucosa	stomach
30	chr11:36394600-36397600	Weak transcription	HSMMtube	muscle
31	chr11:36394800-36396600	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr11:36394800-36397200	Weak transcription	NH-A	brain
33	chr11:36394800-36397400	Weak transcription	Small Intestine	intestine
34	chr11:36394800-36397600	Weak transcription	Brain Anterior Caudate	brain
35	chr11:36394800-36397600	Weak transcription	Brain Substantia Nigra	brain
36	chr11:36394800-36397800	Weak transcription	Pancreas	Pancrea
37	chr11:36395000-36395600	Enhancers	A549	lung
38	chr11:36395000-36397400	Weak transcription	HSMM	muscle
39	chr11:36395000-36397600	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr11:36395200-36395400	Enhancers	Brain Cingulate Gyrus	brain
41	chr11:36395200-36395600	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
42	chr11:36395200-36396200	Enhancers	Rectal Mucosa Donor 29	rectum
43	chr11:36395200-36396400	Weak transcription	Brain Hippocampus Middle	brain
44	chr11:36395200-36397200	Weak transcription	Fetal Kidney	kidney
45	chr11:36395200-36397400	Enhancers	Rectal Mucosa Donor 31	rectum

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