Variant report

Variant	rs56049904
Chromosome Location	chr11:66738987-66738988
allele	C/T
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	MAX	chr11:66736977-66739463	A549	lung:	n/a	n/a
2	CEBPB	chr11:66737711-66739027	HCT-116	colon:	n/a	chr11:66738523-66738536 chr11:66738525-66738534 chr11:66738523-66738534
3	TCF12	chr11:66737089-66739323	A549	lung:	n/a	chr11:66738887-66738897 chr11:66738891-66738898
4	NR2F2	chr11:66738029-66739014	HepG2	liver:	n/a	chr11:66738562-66738577
5	RAD21	chr11:66738106-66739120	IMR90	lung:	n/a	chr11:66738851-66738863 chr11:66738852-66738865
6	EP300	chr11:66737540-66739211	A549	lung:	n/a	n/a
7	NFIC	chr11:66738149-66739010	SK-N-SH	brain:	n/a	n/a
8	SP1	chr11:66737876-66739036	HCT-116	colon:	n/a	n/a
9	MXI1	chr11:66737929-66739191	Hela-S3	cervix:	n/a	n/a
10	MAZ	chr11:66737726-66738987	Hela-S3	cervix:	n/a	n/a
11	TCF7L2	chr11:66737714-66739059	Hela-S3	cervix:	n/a	chr11:66738438-66738447
12	SP1	chr11:66737607-66739054	A549	lung:	n/a	n/a
13	CEBPB	chr11:66737649-66739100	A549	lung:	n/a	chr11:66738523-66738536 chr11:66738525-66738534 chr11:66738523-66738534
14	POLR2A	chr11:66737594-66739298	IMR90	lung:	n/a	n/a
15	GATA3	chr11:66737511-66739291	A549	lung:	n/a	chr11:66738436-66738445
16	SIX5	chr11:66736920-66739489	A549	lung:	n/a	n/a
17	MAX	chr11:66737681-66739202	A549	lung:	n/a	n/a
18	CEBPB	chr11:66737834-66739015	HCT-116	colon:	n/a	chr11:66738523-66738536 chr11:66738525-66738534 chr11:66738523-66738534
19	CTCF	chr11:66738880-66739030	A549	lung:	n/a	n/a
20	BCL3	chr11:66737722-66739103	A549	lung:	n/a	n/a
21	POLR2A	chr11:66738091-66739002	Hela-S3	cervix:	n/a	n/a
22	SMARCC2	chr11:66737906-66739032	Hela-S3	cervix:	n/a	n/a
23	MYC	chr11:66738154-66739100	Hela-S3	cervix:	n/a	n/a
24	ZKSCAN1	chr11:66737800-66739080	Hela-S3	cervix:	n/a	n/a
25	EP300	chr11:66737146-66739146	A549	lung:	n/a	n/a
26	BCL3	chr11:66737671-66739002	A549	lung:	n/a	n/a
27	JUND	chr11:66737737-66739029	HCT-116	colon:	n/a	chr11:66738436-66738447 chr11:66738437-66738447 chr11:66738406-66738417 chr11:66738438-66738446 chr11:66738436-66738448
28	JUND	chr11:66737867-66739300	HCT-116	colon:	n/a	chr11:66738436-66738447 chr11:66738437-66738447 chr11:66738406-66738417 chr11:66738438-66738446 chr11:66738436-66738448
29	SP1	chr11:66737345-66739084	A549	lung:	n/a	n/a
30	POLR2A	chr11:66737884-66739056	Hela-S3	cervix:	n/a	n/a
31	SMC3	chr11:66737710-66739005	Hela-S3	cervix:	n/a	n/a
32	CBX3	chr11:66737515-66739152	HCT-116	colon:	n/a	n/a
33	GTF2F1	chr11:66737734-66739026	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:66646522..66648593-chr11:66737895..66740252,2	K562	blood:
2	chr11:66725578..66729974-chr11:66736794..66740628,4	MCF-7	breast:
3	chr11:66738264..66739924-chr11:66743604..66745176,2	K562	blood:
4	chr11:66736994..66739710-chr11:66794415..66796877,2	MCF-7	breast:
5	chr11:66724086..66726976-chr11:66738899..66741641,2	K562	blood:

Variant related genes	Relation type
C11orf86	TF binding region
ENSG00000173227	Chromatin interaction
ENSG00000173599	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11538048	1.00[AMR][1000 genomes]
rs55962689	1.00[AMR][1000 genomes]
rs56194916	1.00[AMR][1000 genomes]
rs56705397	1.00[AMR][1000 genomes]
rs56728386	1.00[AMR][1000 genomes]
rs57237794	1.00[AMR][1000 genomes]
rs57241231	1.00[AMR][1000 genomes]
rs57508396	1.00[AMR][1000 genomes]
rs57550064	1.00[AMR][1000 genomes]
rs57630565	1.00[AMR][1000 genomes]
rs58201175	1.00[AMR][1000 genomes]
rs59663951	1.00[AMR][1000 genomes]
rs59868470	1.00[AMR][1000 genomes]
rs60523317	1.00[AMR][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	nsv897794	chr11:66579572-66744119	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv555226	chr11:66579572-66845362	Active TSS Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
3	nsv428574	chr11:66619002-66804133	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv832194	chr11:66634462-66805980	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	33 gene(s)	inside rSNPs	diseases
5	nsv531397	chr11:66653381-67465721	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66734800-66739800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr11:66734800-66739800	Enhancers	HMEC	breast
3	chr11:66735000-66739800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr11:66737000-66739800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr11:66737000-66742600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr11:66737000-66742800	Enhancers	Fetal Intestine Large	intestine
7	chr11:66737200-66739000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr11:66737200-66739200	Flanking Active TSS	Hela-S3	cervix
9	chr11:66737200-66739400	Enhancers	Adipose Nuclei	Adipose
10	chr11:66737200-66739800	Enhancers	HSMMtube	muscle
11	chr11:66737200-66740600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr11:66737400-66739000	Enhancers	Small Intestine	intestine
13	chr11:66737400-66739200	Enhancers	Duodenum Mucosa	Duodenum
14	chr11:66737400-66739800	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr11:66737400-66739800	Enhancers	Liver	Liver
16	chr11:66737400-66739800	Enhancers	Monocytes-CD14+_RO01746	blood
17	chr11:66737600-66739200	Enhancers	HUVEC	blood vessel
18	chr11:66737800-66739000	Enhancers	Aorta	Aorta
19	chr11:66737800-66739000	Enhancers	Rectal Mucosa Donor 31	rectum
20	chr11:66738000-66739000	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr11:66738000-66739000	Enhancers	Brain Anterior Caudate	brain
22	chr11:66738000-66739000	Enhancers	Skeletal Muscle Female	skeletal muscle
23	chr11:66738000-66739000	Flanking Active TSS	HepG2	liver
24	chr11:66738000-66739200	Enhancers	Stomach Mucosa	stomach
25	chr11:66738000-66742000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr11:66738200-66739000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr11:66738200-66739000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr11:66738200-66739000	Enhancers	Placenta Amnion	Placenta Amnion
29	chr11:66738200-66739600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr11:66738200-66739600	Enhancers	NHDF-Ad	bronchial
31	chr11:66738200-66739800	Enhancers	Osteobl	bone
32	chr11:66738400-66739000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr11:66738400-66739600	Enhancers	NHLF	lung
34	chr11:66738400-66739800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr11:66738400-66739800	Enhancers	NH-A	brain
36	chr11:66738400-66740200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr11:66738600-66739000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr11:66738600-66739000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr11:66738600-66739000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
40	chr11:66738600-66739000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr11:66738600-66739000	Enhancers	Esophagus	oesophagus
42	chr11:66738600-66739000	Enhancers	Skeletal Muscle Male	skeletal muscle
43	chr11:66738600-66739000	Flanking Active TSS	HSMM	muscle
44	chr11:66738600-66739200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr11:66738600-66739200	Enhancers	Placenta	Placenta
46	chr11:66738600-66739200	Flanking Active TSS	A549	lung
47	chr11:66738600-66739600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr11:66738600-66739800	Enhancers	Fetal Intestine Small	intestine
49	chr11:66738600-66739800	Enhancers	Lung	lung
50	chr11:66738800-66739000	Enhancers	ES-I3 Cell Line	embryonic stem cell

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