Variant report

Variant	rs4541174
Chromosome Location	chr19:56164716-56164717
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:32)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr19:56164580-56164730	BJ	skin:	n/a	n/a
2	HMGN3	chr19:56164368-56166029	K562	blood:	n/a	n/a
3	POLR2A	chr19:56164619-56167840	HepG2	liver:	n/a	n/a
4	POLR2A	chr19:56164429-56167609	K562	blood:	n/a	n/a

No data

(count:32 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:56109380..56112832-chr19:56163189..56166704,4	K562	blood:
2	chr19:56143418..56144411-chr19:56164674..56165216,3	MCF-7	breast:
3	chr19:56164558..56166993-chr20:49346694..49348650,2	MCF-7	breast:
4	chr19:17412304..17413804-chr19:56163545..56165286,2	MCF-7	breast:
5	chr19:55894962..55896497-chr19:56164481..56166264,2	K562	blood:
6	chr19:56110522..56112658-chr19:56163189..56166668,4	K562	blood:
7	chr19:55580785..55582865-chr19:56164262..56165799,2	MCF-7	breast:
8	chr19:55918119..55920865-chr19:56163713..56165863,3	K562	blood:
9	chr19:55591162..55592907-chr19:56164329..56166791,2	K562	blood:
10	chr19:55684227..55686502-chr19:56163659..56165514,2	K562	blood:
11	chr19:56145825..56146505-chr19:56164662..56165252,2	K562	blood:
12	chr19:55986503..55989848-chr19:56164025..56167760,5	K562	blood:
13	chr19:56110653..56113509-chr19:56160158..56165183,5	MCF-7	breast:
14	chr19:55972391..55974736-chr19:56164397..56167331,2	MCF-7	breast:
15	chr1:154989697..154990248-chr19:56164704..56165234,2	MCF-7	breast:
16	chr19:55897327..55900767-chr19:56164045..56167151,4	K562	blood:
17	chr19:56164666..56171824-chr19:56183341..56192911,16	MCF-7	breast:
18	chr19:55970859..55974182-chr19:56164245..56166880,4	K562	blood:
19	chr19:56134460..56137185-chr19:56162633..56166165,3	K562	blood:
20	chr19:55897327..55899035-chr19:56164311..56166921,2	K562	blood:
21	chr19:55994694..55998007-chr19:56163812..56166427,4	K562	blood:
22	chr19:56028047..56028825-chr19:56164679..56165319,2	K562	blood:
23	chr19:56164264..56167135-chr19:56631802..56633967,4	K562	blood:
24	chr19:55894527..55896497-chr19:56163809..56165981,2	K562	blood:
25	chr19:56154378..56155395-chr19:56164636..56165646,5	K562	blood:
26	chr19:56164701..56165323-chr19:56320540..56321426,2	MCF-7	breast:
27	chr19:56164686..56165236-chr19:56205383..56205917,2	MCF-7	breast:
28	chr19:56154666..56155441-chr19:56164653..56165540,4	MCF-7	breast:
29	chr19:56110285..56113089-chr19:56164482..56167654,4	MCF-7	breast:
30	chr19:55579330..55580947-chr19:56164078..56166012,2	MCF-7	breast:
31	chr19:56134221..56137618-chr19:56162633..56168532,10	K562	blood:
32	chr19:56116757..56118714-chr19:56164640..56166848,2	MCF-7	breast:

No data

Variant related genes	Relation type
U2AF2	TF binding region
ENSG00000108107	Chromatin interaction
ENSG00000267523	Chromatin interaction
ENSG00000124171	Chromatin interaction
ENSG00000129990	Chromatin interaction
ENSG00000090971	Chromatin interaction
ENSG00000261221	Chromatin interaction
ENSG00000171425	Chromatin interaction
ENSG00000130312	Chromatin interaction
ENSG00000142409	Chromatin interaction
ENSG00000063245	Chromatin interaction
ENSG00000269859	Chromatin interaction
ENSG00000063241	Chromatin interaction
ENSG00000179943	Chromatin interaction
ENSG00000160439	Chromatin interaction
ENSG00000108106	Chromatin interaction
ENSG00000179922	Chromatin interaction
ENSG00000171443	Chromatin interaction
ENSG00000213015	Chromatin interaction
ENSG00000233493	Chromatin interaction
ENSG00000131037	Chromatin interaction
ENSG00000197483	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11084406	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11665872	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11666362	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11671023	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2112799	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3786650	1.00[ASN][1000 genomes]
rs4801261	1.00[ASN][1000 genomes]
rs73062531	0.92[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:9 , 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	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
8	nsv833882	chr19:56158633-56326564	Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
9	esv3430993	chr19:56163590-56165588	Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4541174	ZNF580	cis	Artery Tibial	GTEx

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56160000-56165200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr19:56160200-56165200	Weak transcription	Small Intestine	intestine
3	chr19:56160400-56165000	Weak transcription	HSMMtube	muscle
4	chr19:56160400-56165200	Weak transcription	NHDF-Ad	bronchial
5	chr19:56160600-56164800	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr19:56160800-56164800	Weak transcription	Fetal Lung	lung
7	chr19:56160800-56165000	Weak transcription	Liver	Liver
8	chr19:56160800-56165200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr19:56160800-56165200	Weak transcription	Gastric	stomach
10	chr19:56160800-56165200	Weak transcription	Left Ventricle	heart
11	chr19:56160800-56165200	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr19:56161000-56164800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr19:56161000-56164800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr19:56161000-56165000	Weak transcription	Primary T cells from cord blood	blood
15	chr19:56161000-56165000	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr19:56161000-56165000	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr19:56161000-56165000	Weak transcription	Fetal Kidney	kidney
18	chr19:56161000-56165200	Weak transcription	Pancreas	Pancrea
19	chr19:56161000-56165200	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr19:56161200-56164800	Weak transcription	Brain Cingulate Gyrus	brain
21	chr19:56161200-56165000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr19:56161200-56165000	Weak transcription	Brain Angular Gyrus	brain
23	chr19:56161200-56165000	Weak transcription	Brain Anterior Caudate	brain
24	chr19:56161200-56165000	Weak transcription	Brain Substantia Nigra	brain
25	chr19:56161200-56165200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr19:56161200-56165200	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr19:56161200-56165200	Weak transcription	Right Atrium	heart
28	chr19:56161200-56165200	Weak transcription	Stomach Mucosa	stomach
29	chr19:56161800-56165200	Weak transcription	Lung	lung
30	chr19:56162000-56165000	Weak transcription	K562	blood
31	chr19:56162200-56165200	Weak transcription	Ovary	ovary
32	chr19:56162600-56164800	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr19:56162800-56164800	Weak transcription	Thymus	Thymus
34	chr19:56163400-56167800	Active TSS	iPS-15b Cell Line	embryonic stem cell
35	chr19:56163400-56168000	Active TSS	H9 Cell Line	embryonic stem cell
36	chr19:56163400-56168200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr19:56163600-56164800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr19:56163600-56167800	Active TSS	ES-I3 Cell Line	embryonic stem cell
39	chr19:56163600-56167800	Active TSS	HUES6 Cell Line	embryonic stem cell
40	chr19:56163600-56168000	Active TSS	HUES64 Cell Line	embryonic stem cell
41	chr19:56163800-56164800	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr19:56163800-56165000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr19:56163800-56165000	Enhancers	Primary T cells fromperipheralblood	blood
44	chr19:56163800-56165000	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr19:56164000-56164800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr19:56164000-56164800	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
47	chr19:56164000-56164800	Enhancers	Fetal Heart	heart
48	chr19:56164000-56164800	Weak transcription	Stomach Smooth Muscle	stomach
49	chr19:56164000-56165000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr19:56164000-56165000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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