Variant report

Variant	rs11154696
Chromosome Location	chr6:133085461-133085462
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	FOS	chr6:133085444-133085966	MCF10A-Er-Src	breast:	n/a	n/a
2	ESR1	chr6:133085202-133085592	T-47D	breast:	n/a	chr6:133085423-133085440 chr6:133085422-133085439
3	STAT3	chr6:133085453-133085853	MCF10A-Er-Src	breast:	n/a	chr6:133085627-133085638 chr6:133085804-133085812
4	FOS	chr6:133085263-133085892	MCF10A-Er-Src	breast:	n/a	n/a
5	FOS	chr6:133085244-133085884	MCF10A-Er-Src	breast:	n/a	n/a
6	ESR1	chr6:133085212-133085536	T-47D	breast:	n/a	chr6:133085423-133085440 chr6:133085422-133085439
7	FOS	chr6:133085440-133086079	MCF10A-Er-Src	breast:	n/a	n/a
8	STAT3	chr6:133085461-133085839	MCF10A-Er-Src	breast:	n/a	chr6:133085627-133085638 chr6:133085804-133085812

No.	Distal block	Cell Line	Cell type
1	chr6:133084415..133087080-chr6:133134762..133137402,2	MCF-7	breast:
2	chr6:133054047..133059196-chr6:133082600..133087082,5	MCF-7	breast:
3	chr6:133084618..133086907-chr6:133118822..133121566,2	K562	blood:
4	chr6:133084942..133087324-chr6:133134860..133137280,2	MCF-7	breast:

Variant related genes	Relation type
VNN2	TF binding region
ENSG00000271488	TF binding region
ENSG00000093134	Chromatin interaction
ENSG00000146409	Chromatin interaction
ENSG00000112306	Chromatin interaction
ENSG00000206754	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs12202302	0.89[CEU][hapmap];0.89[CHB][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];0.87[JPT][hapmap];0.96[MEX][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1983607	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2236381	0.91[MEX][hapmap]
rs2236382	0.91[MEX][hapmap]
rs3756969	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3778174	0.81[EUR][1000 genomes]
rs4599669	0.91[MEX][hapmap]
rs6917833	0.80[CHB][hapmap]
rs6926466	0.89[CEU][hapmap];0.89[CHB][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];0.87[JPT][hapmap];0.96[MEX][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs761125	0.92[ASW][hapmap];0.94[CEU][hapmap];0.89[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.87[JPT][hapmap];0.86[LWK][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7751879	0.89[CHB][hapmap]
rs9321374	0.91[MEX][hapmap]
rs9375921	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9375927	0.84[MEX][hapmap]
rs9389034	0.91[MEX][hapmap]
rs9493451	0.89[CEU][hapmap];0.89[CHB][hapmap];0.85[JPT][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9493458	0.83[MEX][hapmap]
rs9493459	0.82[CHD][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap]

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	nsv532069	chr6:132776411-133462292	Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv1015742	chr6:132933666-133285852	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11154696	SNORA33	cis	cerebellum	SCAN

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:133061400-133098000	Weak transcription	Spleen	Spleen
2	chr6:133065000-133098000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr6:133081400-133096800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr6:133081800-133086800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr6:133083200-133085800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
6	chr6:133083200-133086000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr6:133083200-133086600	Enhancers	Fetal Intestine Large	intestine
8	chr6:133083400-133090600	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr6:133083600-133099000	Weak transcription	Left Ventricle	heart
10	chr6:133083800-133118200	Weak transcription	Brain Cingulate Gyrus	brain
11	chr6:133084000-133089000	Weak transcription	Fetal Intestine Small	intestine
12	chr6:133084400-133085800	Enhancers	Placenta	Placenta
13	chr6:133084600-133085800	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr6:133084600-133085800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
15	chr6:133084600-133085800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr6:133084600-133086000	Enhancers	Primary neutrophils fromperipheralblood	blood
17	chr6:133084600-133087000	Enhancers	Fetal Stomach	stomach
18	chr6:133084600-133091200	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr6:133084800-133085600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr6:133084800-133085600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
21	chr6:133084800-133085600	Enhancers	Primary T helper cells fromperipheralblood	blood
22	chr6:133084800-133085600	Enhancers	Stomach Mucosa	stomach
23	chr6:133084800-133085800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr6:133084800-133086400	Enhancers	HMEC	breast
25	chr6:133084800-133086400	Enhancers	NHLF	lung
26	chr6:133084800-133089400	Weak transcription	Fetal Thymus	thymus
27	chr6:133084800-133091800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr6:133084800-133097000	Weak transcription	Fetal Muscle Leg	muscle
29	chr6:133085000-133085600	Enhancers	Primary T helper naive cells from peripheral blood	blood
30	chr6:133085000-133085600	Enhancers	Colon Smooth Muscle	Colon
31	chr6:133085000-133085600	Enhancers	A549	lung
32	chr6:133085000-133085600	Enhancers	Monocytes-CD14+_RO01746	blood
33	chr6:133085000-133085800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
34	chr6:133085000-133085800	Enhancers	Primary T killer memory cells from peripheral blood	blood
35	chr6:133085000-133085800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr6:133085000-133086000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr6:133085000-133086000	Enhancers	Hela-S3	cervix
38	chr6:133085000-133086000	Enhancers	NHEK	skin
39	chr6:133085000-133086400	Enhancers	Adipose Nuclei	Adipose
40	chr6:133085000-133086600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr6:133085000-133086600	Enhancers	NHDF-Ad	bronchial
42	chr6:133085000-133109000	Weak transcription	GM12878-XiMat	blood
43	chr6:133085000-133114600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr6:133085000-133119000	Weak transcription	Thymus	Thymus
45	chr6:133085200-133085800	Enhancers	Aorta	Aorta
46	chr6:133085200-133086000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr6:133085200-133086000	Enhancers	HSMMtube	muscle
48	chr6:133085200-133086000	Enhancers	NH-A	brain
49	chr6:133085200-133086200	Enhancers	Muscle Satellite Cultured Cells	--
50	chr6:133085200-133086200	Enhancers	Osteobl	bone

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