Variant report

Variant	rs11084406
Chromosome Location	chr19:56156447-56156448
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:45)
CpG islands
(count:61)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:56156051-56157199	GM12892	blood:	n/a	n/a
2	POLR2A	chr19:56150319-56156666	Hela-S3	cervix:	n/a	n/a
3	TCF12	chr19:56155970-56156738	ECC-1	luminal epithelium:	n/a	n/a
4	POLR2A	chr19:56150192-56156534	GM12878	blood:	n/a	n/a
5	EP300	chr19:56156148-56156594	ECC-1	luminal epithelium:	n/a	n/a
6	POLR2A	chr19:56156383-56156739	GM12878	blood:	n/a	n/a
7	RUNX3	chr19:56156122-56156526	GM12878	blood:	n/a	n/a
8	POLR2A	chr19:56149778-56157300	PANC-1	pancreas:	n/a	n/a
9	ESR1	chr19:56156184-56156523	ECC-1	luminal epithelium:	n/a	n/a
10	POLR2A	chr19:56150010-56156634	MCF10A-Er-Src	breast:	n/a	n/a
11	PAX5	chr19:56155991-56156526	GM12878	blood:	n/a	n/a
12	POLR2A	chr19:56151325-56156943	GM19099	blood:	n/a	n/a
13	POLR2A	chr19:56156106-56157150	HepG2	liver:	n/a	n/a
14	ZNF263	chr19:56154054-56156500	HEK293-T-REx	kidney:	n/a	n/a
15	ELF1	chr19:56155707-56156676	GM12878	blood:	n/a	n/a
16	POLR2A	chr19:56155829-56157111	GM12878	blood:	n/a	n/a
17	POLR2A	chr19:56151378-56156635	GM18951	blood:	n/a	n/a
18	POLR2A	chr19:56151310-56156615	Raji	blood:	n/a	n/a
19	POLR2A	chr19:56151262-56156558	GM12878	blood:	n/a	n/a
20	PAX5	chr19:56156202-56156481	GM12892	blood:	n/a	n/a
21	PAX5	chr19:56156107-56156456	GM12878	blood:	n/a	n/a
22	POLR2A	chr19:56150387-56157088	GM18505	blood:	n/a	n/a
23	POLR2A	chr19:56151277-56156546	GM15510	blood:	n/a	n/a
24	POLR2A	chr19:56151284-56157050	GM19193	blood:	n/a	n/a
25	TCF3	chr19:56156144-56156465	GM12878	blood:	n/a	n/a
26	POLR2A	chr19:56156216-56156832	ECC-1	luminal epithelium:	n/a	n/a
27	EP300	chr19:56155906-56156789	ECC-1	luminal epithelium:	n/a	n/a
28	TCF12	chr19:56155937-56156755	ECC-1	luminal epithelium:	n/a	n/a
29	EBF1	chr19:56156231-56156504	GM12878	blood:	n/a	n/a
30	POLR2A	chr19:56156066-56157076	K562	blood:	n/a	n/a
31	POLR2A	chr19:56151126-56156975	K562	blood:	n/a	n/a
32	POLR2A	chr19:56153924-56157156	GM12892	blood:	n/a	n/a
33	NFATC1	chr19:56155808-56156461	GM12878	blood:	n/a	n/a
34	POLR2A	chr19:56151411-56156949	Hela-S3	cervix:	n/a	n/a
35	RUNX3	chr19:56156205-56156478	GM12878	blood:	n/a	n/a
36	MAX	chr19:56156070-56156645	ECC-1	luminal epithelium:	n/a	n/a
37	POLR2A	chr19:56156305-56156530	H1-hESC	embryonic stem cell:	n/a	n/a
38	PML	chr19:56156080-56156747	GM12878	blood:	n/a	n/a
39	POLR2A	chr19:56151218-56156671	HL-60	blood:	n/a	n/a
40	POLR2A	chr19:56153842-56156741	GM12878	blood:	n/a	n/a
41	POLR2A	chr19:56151178-56157193	GM12878	blood:	n/a	n/a
42	EBF1	chr19:56156129-56156574	GM12878	blood:	n/a	n/a
43	PAX5	chr19:56156169-56156502	GM12878	blood:	n/a	n/a
44	POLR2A	chr19:56155969-56157007	GM12891	blood:	n/a	n/a
45	NFIC	chr19:56155989-56156685	ECC-1	luminal epithelium:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:56156430-56156480	A549	lung:	n/a
2	chr19:56156430-56156480	T-47D	breast:	n/a
3	chr19:56156430-56156480	HCM	heart:	n/a
4	chr19:56156430-56156480	SK-N-MC	brain:	n/a
5	chr19:56156430-56156480	AG10803	skin:	n/a
6	chr19:56156430-56156480	HRCEpiC	kidney:	n/a
7	chr19:56156430-56156480	AoSMC	blood vessel:	n/a
8	chr19:56156430-56156480	HCPEpiC	choroid plexus:	n/a
9	chr19:56156430-56156480	Jurkat	blood:	n/a
10	chr19:56156430-56156480	SK-N-SH	brain:	n/a
11	chr19:56156430-56156480	HNPCEpiC	eye:	n/a
12	chr19:56156430-56156480	PFSK-1	brain:	n/a
13	chr19:56156430-56156480	NT2-D1	testis:	n/a
14	chr19:56156430-56156480	H1-hESC	embryonic stem cell:	embryo
15	chr19:56156430-56156480	HMEC	breast:	n/a
16	chr19:56156430-56156480	Hepatocyte	liver:	n/a
17	chr19:56156430-56156480	HepG2	liver:	n/a
18	chr19:56156430-56156480	AG09309	skin:	n/a
19	chr19:56156430-56156480	SAEC	small airway:	n/a
20	chr19:56156430-56156480	HUVEC	blood vessel:	n/a
21	chr19:56156430-56156480	HRPEpiC	eye:	n/a
22	chr19:56156430-56156480	NHDF-neo	bronchial:	n/a
23	chr19:56156430-56156480	K562	blood:	n/a
24	chr19:56156430-56156480	HRE	kidney:	n/a
25	chr19:56156430-56156480	NH-A	brain:	n/a
26	chr19:56156430-56156480	MCF10A-Er-Src	breast:	n/a
27	chr19:56156430-56156480	SK-N-SH_RA	brain:	n/a
28	chr19:56156430-56156480	AG04450	lung:	fetal
29	chr19:56156430-56156480	U87	brain:	n/a
30	chr19:56156430-56156480	HEEpiC	esophagus:	n/a
31	chr19:56156430-56156480	ECC-1	luminal epithelium:	n/a
32	chr19:56156430-56156480	HPAEpiC	pulmonary alveolar:	n/a
33	chr19:56156430-56156480	RPTEC	kidney:	n/a
34	chr19:56156430-56156480	HIPEpiC	eye:	n/a
35	chr19:56156430-56156480	GM19239	blood:	n/a
36	chr19:56156430-56156480	Hela-S3	cervix:	n/a
37	chr19:56156430-56156480	GM12892	blood:	n/a
38	chr19:56156430-56156480	Caco-2	colon:	n/a
39	chr19:56156430-56156480	HCF	heart:	n/a
40	chr19:56156430-56156480	AG04449	skin:	fetal
41	chr19:56156430-56156480	HCT-116	colon:	n/a
42	chr19:56156430-56156480	CMK	blood:	n/a
43	chr19:56156430-56156480	NB4	blood:	n/a
44	chr19:56156430-56156480	GM12891	blood:	n/a
45	chr19:56156430-56156480	GM12878	blood:	n/a
46	chr19:56156430-56156480	HAEpiC	amniotic membrane:	n/a
47	chr19:56156430-56156480	IMR90	lung:	fetal
48	chr19:56156430-56156480	HEK293	kidney:	embryo
49	chr19:56156430-56156480	PANC-1	pancreas:	n/a
50	chr19:56156430-56156480	MCF-7	breast:	n/a

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:56132811..56137423-chr19:56151241..56156557,5	MCF-7	breast:
2	chr19:56154949..56157092-chr19:56632186..56634615,2	K562	blood:
3	chr19:56154222..56156750-chr19:56202512..56205168,2	K562	blood:
4	chr19:55918058..55920032-chr19:56154826..56156476,2	MCF-7	breast:
5	chr19:56009548..56011296-chr19:56155701..56158462,2	K562	blood:

No data

Variant related genes	Relation type
CCDC106	TF binding region
CCDC106	CpG island
ENSG00000179922	Chromatin interaction
ENSG00000108106	Chromatin interaction
ENSG00000063245	Chromatin interaction
ENSG00000142409	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11665872	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11666362	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11671023	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11882068	0.80[TSI][hapmap]
rs2112799	1.00[CEU][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3786650	1.00[ASN][1000 genomes]
rs4541174	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4801261	0.81[CEU][hapmap];1.00[ASN][1000 genomes]
rs73062531	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73062564	1.00[ASN][1000 genomes]
rs8104386	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912487	chr19:55977909-56215184	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
2	nsv912494	chr19:56026072-56215184	Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
3	nsv912498	chr19:56041848-56215184	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
4	nsv912500	chr19:56078722-56175515	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	86 gene(s)	inside rSNPs	diseases
5	nsv912501	chr19:56093365-56215184	Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
6	nsv428026	chr19:56130849-56423514	Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	82 gene(s)	inside rSNPs	diseases
7	nsv912503	chr19:56149077-56162776	Genic enhancers Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	30 gene(s)	inside rSNPs	diseases
8	nsv912504	chr19:56149077-56170415	Flanking Active TSS Genic enhancers Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11084406	ZNF580	cis	Artery Tibial	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56155600-56157000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr19:56155800-56156600	Weak transcription	Fetal Kidney	kidney
3	chr19:56155800-56156800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
4	chr19:56155800-56156800	Enhancers	Fetal Heart	heart
5	chr19:56155800-56157000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr19:56155800-56157000	Genic enhancers	Fetal Muscle Trunk	muscle
7	chr19:56155800-56157000	Genic enhancers	Gastric	stomach
8	chr19:56155800-56157200	Genic enhancers	Primary T cells from cord blood	blood
9	chr19:56155800-56157400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr19:56155800-56158800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr19:56156000-56156600	Transcr. at gene 5' and 3'	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr19:56156000-56156600	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
13	chr19:56156000-56156600	Enhancers	Primary T killer memory cells from peripheral blood	blood
14	chr19:56156000-56156600	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr19:56156000-56156600	Genic enhancers	Colonic Mucosa	Colon
16	chr19:56156000-56156600	Genic enhancers	Ovary	ovary
17	chr19:56156000-56156600	Genic enhancers	Pancreas	Pancrea
18	chr19:56156000-56156800	Genic enhancers	Primary B cells from cord blood	blood
19	chr19:56156000-56156800	Genic enhancers	Primary T cells fromperipheralblood	blood
20	chr19:56156000-56156800	Genic enhancers	Cortex derived primary cultured neurospheres	brain
21	chr19:56156000-56156800	Genic enhancers	Brain Angular Gyrus	brain
22	chr19:56156000-56156800	Genic enhancers	Fetal Muscle Leg	muscle
23	chr19:56156000-56156800	Genic enhancers	Fetal Thymus	thymus
24	chr19:56156000-56156800	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
25	chr19:56156000-56156800	Transcr. at gene 5' and 3'	HMEC	breast
26	chr19:56156000-56156800	Transcr. at gene 5' and 3'	NHEK	skin
27	chr19:56156000-56157000	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr19:56156000-56157000	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
29	chr19:56156000-56157000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
30	chr19:56156000-56157000	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr19:56156000-56157000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr19:56156000-56157000	Genic enhancers	Right Ventricle	heart
33	chr19:56156000-56157000	Transcr. at gene 5' and 3'	Skeletal Muscle Female	skeletal muscle
34	chr19:56156000-56157000	Transcr. at gene 5' and 3'	Dnd41	blood
35	chr19:56156000-56157000	Transcr. at gene 5' and 3'	Hela-S3	cervix
36	chr19:56156000-56157200	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr19:56156000-56157200	Strong transcription	H9 Cell Line	embryonic stem cell
38	chr19:56156000-56157200	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr19:56156000-56157200	Genic enhancers	Primary B cells from peripheral blood	blood
40	chr19:56156000-56157800	Genic enhancers	Adipose Nuclei	Adipose
41	chr19:56156000-56157800	Genic enhancers	Placenta	Placenta
42	chr19:56156000-56158600	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr19:56156000-56158600	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr19:56156000-56158800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr19:56156200-56156600	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr19:56156200-56156600	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr19:56156200-56156600	Weak transcription	Colon Smooth Muscle	Colon
48	chr19:56156200-56156600	Genic enhancers	Rectal Mucosa Donor 29	rectum
49	chr19:56156200-56156800	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
50	chr19:56156200-56156800	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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