Variant report

Variant	rs11667786
Chromosome Location	chr19:56118243-56118244
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:19)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:19 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZC3H11A	chr19:56118175-56118273	K562	blood:	n/a	n/a
2	CTCF	chr19:56118240-56118390	HAc	cerebellar:	n/a	n/a
3	POLR2A	chr19:56115859-56118733	MCF10A-Er-Src	breast:	n/a	n/a
4	RFX5	chr19:56115868-56118564	IMR90	lung:	n/a	n/a
5	POLR2A	chr19:56115967-56118680	MCF10A-Er-Src	breast:	n/a	n/a
6	RCOR1	chr19:56117029-56118333	IMR90	lung:	n/a	n/a
7	ZNF263	chr19:56117404-56118640	HEK293-T-REx	kidney:	n/a	chr19:56117757-56117778
8	POLR2A	chr19:56115759-56118660	PANC-1	pancreas:	n/a	n/a
9	POLR2A	chr19:56115985-56118247	PBDE	blood:	n/a	n/a
10	SMARCC1	chr19:56117169-56118379	Hela-S3	cervix:	n/a	n/a
11	SMC3	chr19:56115894-56118485	SK-N-SH	brain:	n/a	chr19:56116194-56116204 chr19:56116687-56116697 chr19:56116880-56116888 chr19:56116877-56116887
12	HCFC1	chr19:56115872-56118473	Hela-S3	cervix:	n/a	n/a
13	CHD1	chr19:56115950-56118548	IMR90	lung:	n/a	chr19:56116997-56117007
14	WRNIP1	chr19:56117241-56118323	GM12878	blood:	n/a	n/a
15	RFX5	chr19:56115785-56119064	SK-N-SH	brain:	n/a	n/a
16	POLR2A	chr19:56118017-56118273	HUVEC	blood vessel:	n/a	n/a
17	POLR2A	chr19:56115927-56118346	Hela-S3	cervix:	n/a	n/a
18	CTCF	chr19:56117063-56118300	A549	lung:	n/a	chr19:56117071-56117084 chr19:56117743-56117759
19	POLR2A	chr19:56115880-56118358	Hela-S3	cervix:	n/a	n/a

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:55917489..55920268-chr19:56117459..56120602,3	MCF-7	breast:
2	chr19:55917805..55920377-chr19:56116633..56119121,2	K562	blood:
3	chr19:55850159..55852267-chr19:56116484..56118952,2	MCF-7	breast:
4	chr19:55917466..55919305-chr19:56117556..56119630,3	K562	blood:
5	chr19:56116757..56118714-chr19:56164640..56166848,2	MCF-7	breast:
6	chr19:56115235..56119649-chr19:56131831..56136050,11	K562	blood:
7	chr19:56115993..56118637-chr19:56165089..56166891,2	K562	blood:
8	chr19:55895958..55898532-chr19:56117459..56119251,2	MCF-7	breast:
9	chr19:56116914..56119642-chr19:56129157..56131500,3	K562	blood:
10	chr19:55963302..55966247-chr19:56117122..56119582,2	K562	blood:
11	chr19:55971554..55973969-chr19:56116219..56118997,2	MCF-7	breast:
12	chr19:56116994..56118715-chr19:56119312..56122594,3	MCF-7	breast:
13	chr19:56027041..56027915-chr19:56117311..56118272,2	K562	blood:
14	chr19:56116188..56118514-chr19:56134480..56137487,3	MCF-7	breast:
15	chr19:56116639..56119326-chr19:56146420..56148377,2	K562	blood:

No data

Variant related genes	Relation type
FIZ1	TF binding region
ENSG00000179922	Chromatin interaction
ENSG00000063244	Chromatin interaction
ENSG00000133247	Chromatin interaction
ENSG00000063241	Chromatin interaction
ENSG00000267531	Chromatin interaction
ENSG00000108107	Chromatin interaction
ENSG00000171425	Chromatin interaction
ENSG00000233493	Chromatin interaction
ENSG00000108106	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1053817	1.00[ASW][hapmap];1.00[ASN][1000 genomes]
rs11666636	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11668752	1.00[ASW][hapmap];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11669643	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11671353	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11671421	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11671545	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2902747	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4331432	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60547841	1.00[ASN][1000 genomes]
rs73058305	1.00[ASN][1000 genomes]
rs73058308	1.00[ASN][1000 genomes]
rs73058310	1.00[ASN][1000 genomes]
rs73612853	1.00[ASN][1000 genomes]
rs8100277	1.00[ASN][1000 genomes]
rs8109904	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912473	chr19:55874642-56145428	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
2	nsv912486	chr19:55977909-56145428	Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
3	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
4	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
5	nsv912495	chr19:56033088-56132661	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	nsv912496	chr19:56040051-56145428	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
7	nsv912497	chr19:56041848-56145428	Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
8	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
9	nsv828643	chr19:56059280-56154823	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
10	nsv912499	chr19:56071293-56132487	Flanking Active TSS Genic enhancers Active TSS Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
11	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
12	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
13	nsv912502	chr19:56099884-56138575	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11667786	ZNF497	cis	parietal	SCAN
rs11667786	ZNF772	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56117200-56118400	Flanking Active TSS	Fetal Thymus	thymus
2	chr19:56117200-56118600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
3	chr19:56117400-56118400	Flanking Active TSS	Stomach Mucosa	stomach
4	chr19:56117400-56118400	Flanking Active TSS	Stomach Smooth Muscle	stomach
5	chr19:56117600-56118400	Flanking Active TSS	Primary T cells from cord blood	blood
6	chr19:56117600-56118400	Flanking Active TSS	Rectal Smooth Muscle	rectum
7	chr19:56117600-56118400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
8	chr19:56117600-56118600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr19:56117600-56118600	Flanking Active TSS	Brain Anterior Caudate	brain
10	chr19:56117600-56124800	Weak transcription	Small Intestine	intestine
11	chr19:56117800-56118400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
12	chr19:56117800-56118400	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
13	chr19:56117800-56118400	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr19:56117800-56118400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
15	chr19:56117800-56118400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
16	chr19:56117800-56118400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
17	chr19:56117800-56118400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr19:56117800-56118400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
19	chr19:56117800-56118400	Flanking Active TSS	Brain Hippocampus Middle	brain
20	chr19:56117800-56118400	Transcr. at gene 5' and 3'	Brain Inferior Temporal Lobe	brain
21	chr19:56117800-56118400	Transcr. at gene 5' and 3'	Brain Dorsolateral Prefrontal Cortex	brain
22	chr19:56117800-56118400	Flanking Active TSS	Colon Smooth Muscle	Colon
23	chr19:56117800-56118400	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
24	chr19:56117800-56118400	Flanking Active TSS	HSMM	muscle
25	chr19:56117800-56118400	Flanking Active TSS	NHDF-Ad	bronchial
26	chr19:56117800-56118400	Transcr. at gene 5' and 3'	NHLF	lung
27	chr19:56117800-56118600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr19:56117800-56118600	Transcr. at gene 5' and 3'	Dnd41	blood
29	chr19:56117800-56118600	Flanking Active TSS	GM12878-XiMat	blood
30	chr19:56117800-56118600	Flanking Active TSS	Hela-S3	cervix
31	chr19:56117800-56118600	Flanking Active TSS	HMEC	breast
32	chr19:56117800-56119000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr19:56118000-56118400	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr19:56118000-56118400	Transcr. at gene 5' and 3'	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr19:56118000-56118400	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr19:56118000-56118400	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
37	chr19:56118000-56118400	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
38	chr19:56118000-56118400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
39	chr19:56118000-56118400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr19:56118000-56118400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
41	chr19:56118000-56118400	Enhancers	Brain Substantia Nigra	brain
42	chr19:56118000-56118400	Enhancers	Colonic Mucosa	Colon
43	chr19:56118000-56118400	Transcr. at gene 5' and 3'	Duodenum Smooth Muscle	Duodenum
44	chr19:56118000-56118400	Enhancers	Esophagus	oesophagus
45	chr19:56118000-56118400	Genic enhancers	Fetal Muscle Trunk	muscle
46	chr19:56118000-56118400	Enhancers	Lung	lung
47	chr19:56118000-56118400	Enhancers	Rectal Mucosa Donor 31	rectum
48	chr19:56118000-56118400	Enhancers	Right Atrium	heart
49	chr19:56118000-56118400	Genic enhancers	Sigmoid Colon	Sigmoid Colon
50	chr19:56118000-56118400	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle

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