Variant report

Variant	rs1053817
Chromosome Location	chr19:56089219-56089220
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:56088914-56089231	HepG2	liver:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:56086664..56089219-chr19:56150784..56152646,2	MCF-7	breast:
2	chr19:56087628..56093963-chr19:56108517..56113906,9	MCF-7	breast:
3	chr19:56076616..56078313-chr19:56088787..56090501,2	K562	blood:
4	chr19:55916968..55919550-chr19:56086420..56090390,4	K562	blood:
5	chr19:56089123..56090949-chr2:85134145..85135899,2	MCF-7	breast:
6	chr19:56087478..56090277-chr19:56092054..56093869,2	MCF-7	breast:
7	chr19:56087311..56094258-chr19:56108819..56113699,11	K562	blood:
8	chr19:55916968..55919340-chr19:56087208..56090390,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000267730	TF binding region
ENSG00000108106	Chromatin interaction
ENSG00000213015	Chromatin interaction
ENSG00000171425	Chromatin interaction
ENSG00000179943	Chromatin interaction
ENSG00000173581	Chromatin interaction
ENSG00000171443	Chromatin interaction
ENSG00000218891	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11666636	1.00[ASN][1000 genomes]
rs11667786	1.00[ASW][hapmap];1.00[ASN][1000 genomes]
rs11668752	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap];1.00[ASN][1000 genomes]
rs11669643	1.00[ASN][1000 genomes]
rs11671353	1.00[ASN][1000 genomes]
rs11671421	1.00[ASN][1000 genomes]
rs11671545	1.00[ASN][1000 genomes]
rs2902747	1.00[ASN][1000 genomes]
rs4331432	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	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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	esv3388302	chr19:56088140-56092838	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
13	esv3423073	chr19:56088190-56091888	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
14	esv3437537	chr19:56088665-56091513	Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1053817	ZNF497	cis	parietal	SCAN

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56075800-56090400	Weak transcription	Psoas Muscle	Psoas
2	chr19:56076000-56091000	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr19:56076000-56091000	Weak transcription	Right Atrium	heart
4	chr19:56076600-56091000	Weak transcription	Fetal Heart	heart
5	chr19:56078600-56091000	Weak transcription	Fetal Kidney	kidney
6	chr19:56081800-56091000	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr19:56083800-56091000	Weak transcription	HepG2	liver
8	chr19:56084200-56091000	Weak transcription	K562	blood
9	chr19:56085200-56090000	Weak transcription	Fetal Lung	lung
10	chr19:56086000-56090000	Weak transcription	Stomach Smooth Muscle	stomach
11	chr19:56086000-56091000	Weak transcription	NH-A	brain
12	chr19:56086200-56091000	Weak transcription	Rectal Smooth Muscle	rectum
13	chr19:56086200-56091200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr19:56086400-56091200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr19:56086600-56091000	Weak transcription	Fetal Brain Male	brain
16	chr19:56086600-56091400	Weak transcription	Primary T cells from cord blood	blood
17	chr19:56086800-56090600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr19:56086800-56091000	Weak transcription	Brain Substantia Nigra	brain
19	chr19:56086800-56091000	Weak transcription	HMEC	breast
20	chr19:56087000-56091000	Weak transcription	Duodenum Mucosa	Duodenum
21	chr19:56087000-56091200	Weak transcription	Stomach Mucosa	stomach
22	chr19:56087200-56090000	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr19:56087200-56091000	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr19:56087200-56091000	Weak transcription	GM12878-XiMat	blood
25	chr19:56087200-56091200	Weak transcription	Fetal Thymus	thymus
26	chr19:56087400-56089400	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr19:56087400-56089400	Strong transcription	Fetal Muscle Trunk	muscle
28	chr19:56087400-56090000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr19:56087400-56090000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr19:56087400-56090200	Strong transcription	Fetal Intestine Large	intestine
31	chr19:56087400-56090400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr19:56087400-56090400	Strong transcription	Brain Germinal Matrix	brain
33	chr19:56087400-56090400	Strong transcription	Fetal Muscle Leg	muscle
34	chr19:56087400-56090600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr19:56087400-56090600	Strong transcription	Cortex derived primary cultured neurospheres	brain
36	chr19:56087400-56090600	Strong transcription	Fetal Brain Female	brain
37	chr19:56087600-56089400	Strong transcription	HUES6 Cell Line	embryonic stem cell
38	chr19:56087600-56089400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr19:56087600-56089400	Strong transcription	Fetal Intestine Small	intestine
40	chr19:56087600-56090200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr19:56087600-56090200	Strong transcription	A549	lung
42	chr19:56087600-56090600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr19:56087600-56090600	Strong transcription	Fetal Stomach	stomach
44	chr19:56087600-56090800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr19:56087600-56090800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr19:56087600-56091400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr19:56087800-56090800	Weak transcription	Hela-S3	cervix
48	chr19:56088000-56089600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
49	chr19:56088000-56090400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr19:56088000-56090600	Strong transcription	Duodenum Smooth Muscle	Duodenum

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