Variant report

Variant	rs3020061
Chromosome Location	chr11:93063200-93063201
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	MAZ	chr11:93063189-93064233	K562	blood:	n/a	chr11:93063738-93063747
2	E2F6	chr11:93063177-93064200	K562	blood:	n/a	chr11:93063682-93063692 chr11:93063676-93063686 chr11:93063767-93063778 chr11:93063679-93063689
3	CUX1	chr11:93063168-93063627	K562	blood:	n/a	n/a
4	UBTF	chr11:93063141-93063824	K562	blood:	n/a	n/a
5	ATF1	chr11:93063176-93063364	K562	blood:	n/a	n/a
6	CBX3	chr11:93063074-93063896	K562	blood:	n/a	n/a
7	UBTF	chr11:93063148-93064078	K562	blood:	n/a	n/a
8	MAX	chr11:93063069-93064301	H1-hESC	embryonic stem cell:	n/a	chr11:93063738-93063747
9	MAX	chr11:93063180-93063759	H1-hESC	embryonic stem cell:	n/a	chr11:93063738-93063747
10	TBP	chr11:93063161-93064139	K562	blood:	n/a	n/a
11	RCOR1	chr11:93063184-93063697	K562	blood:	n/a	n/a
12	RCOR1	chr11:93063078-93064572	K562	blood:	n/a	n/a
13	SIN3A	chr11:93063156-93063892	H1-hESC	embryonic stem cell:	n/a	chr11:93063671-93063680 chr11:93063293-93063304
14	E2F6	chr11:93063176-93064262	H1-hESC	embryonic stem cell:	n/a	chr11:93063682-93063692 chr11:93063676-93063686 chr11:93063767-93063778 chr11:93063679-93063689
15	MYC	chr11:93063197-93064175	K562	blood:	n/a	chr11:93063738-93063747
16	POLR2A	chr11:93063012-93063448	H1-neurons	neurons:	n/a	n/a
17	PML	chr11:93063159-93063817	K562	blood:	n/a	n/a

Variant related genes	Relation type
CCDC67	TF binding region

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11600203	0.86[CHB][hapmap]
rs2605574	0.81[LWK][hapmap]
rs3019208	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3019209	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3019211	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3019212	0.95[CEU][hapmap];0.97[GIH][hapmap];0.81[LWK][hapmap];0.83[MEX][hapmap];0.84[MKK][hapmap];0.87[TSI][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3019213	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3020050	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3020052	1.00[CHB][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3020053	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3020054	1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3020062	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3020064	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3020065	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3020066	0.96[CEU][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3020067	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3020069	0.96[CEU][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3133444	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3133454	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6483233	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7118644	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1039134	chr11:92790000-93219942	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv438	chr11:93034411-93080513	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv898180	chr11:93045561-93082053	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3020061	CCDC67	cis	Thyroid	GTEx

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:93062600-93063200	Bivalent Enhancer	Fetal Heart	heart
2	chr11:93062800-93064600	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr11:93063000-93063200	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
4	chr11:93063000-93063200	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
5	chr11:93063000-93063200	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr11:93063000-93063200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr11:93063000-93063200	Enhancers	Adipose Nuclei	Adipose
8	chr11:93063000-93063200	Active TSS	Duodenum Mucosa	Duodenum
9	chr11:93063000-93063200	Enhancers	Pancreas	Pancrea
10	chr11:93063000-93063200	Bivalent/Poised TSS	NHEK	skin
11	chr11:93063000-93063400	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
12	chr11:93063000-93063400	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
13	chr11:93063000-93063400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr11:93063000-93063600	Flanking Active TSS	K562	blood
15	chr11:93063000-93063800	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr11:93063000-93064000	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr11:93063000-93064200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
18	chr11:93063000-93064200	Bivalent/Poised TSS	Fetal Brain Female	brain
19	chr11:93063000-93064200	Bivalent Enhancer	Placenta	Placenta
20	chr11:93063000-93064400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
21	chr11:93063000-93064600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
22	chr11:93063200-93063400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr11:93063200-93063400	Flanking Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr11:93063200-93063400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
25	chr11:93063200-93063400	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr11:93063200-93063400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr11:93063200-93063400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
28	chr11:93063200-93063400	Flanking Bivalent TSS/Enh	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr11:93063200-93063400	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr11:93063200-93063400	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
31	chr11:93063200-93063400	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
32	chr11:93063200-93063400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr11:93063200-93063400	Flanking Active TSS	Adipose Nuclei	Adipose
34	chr11:93063200-93063400	Active TSS	Brain Germinal Matrix	brain
35	chr11:93063200-93063400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
36	chr11:93063200-93063400	Bivalent Enhancer	Esophagus	oesophagus
37	chr11:93063200-93063400	Flanking Active TSS	Fetal Brain Male	brain
38	chr11:93063200-93063400	Flanking Bivalent TSS/Enh	Fetal Heart	heart
39	chr11:93063200-93063400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
40	chr11:93063200-93063400	Active TSS	Fetal Stomach	stomach
41	chr11:93063200-93063400	Enhancers	Gastric	stomach
42	chr11:93063200-93063400	Flanking Active TSS	Pancreas	Pancrea
43	chr11:93063200-93063400	Enhancers	Placenta Amnion	Placenta Amnion
44	chr11:93063200-93063400	Bivalent Enhancer	Psoas Muscle	Psoas
45	chr11:93063200-93063400	Enhancers	Right Ventricle	heart
46	chr11:93063200-93063400	Bivalent/Poised TSS	GM12878-XiMat	blood
47	chr11:93063200-93063400	Bivalent Enhancer	NH-A	brain
48	chr11:93063200-93063600	Active TSS	Breast Myoepithelial Primary Cells	Breast
49	chr11:93063200-93063600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr11:93063200-93063600	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin

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