Variant report

Variant	rs56937816
Chromosome Location	chr19:52075224-52075225
allele	A/C
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	MTA3	chr19:52074163-52075563	GM12878	blood:	n/a	n/a
2	POLR2A	chr19:52074025-52077434	U87	brain:	n/a	n/a
3	UBTF	chr19:52074244-52075240	K562	blood:	n/a	n/a
4	CUX1	chr19:52074924-52075423	K562	blood:	n/a	n/a
5	GABPA	chr19:52073937-52075247	A549	lung:	n/a	chr19:52074457-52074471 chr19:52074460-52074474 chr19:52074460-52074471
6	POLR2A	chr19:52075219-52076089	K562	blood:	n/a	n/a
7	MAZ	chr19:52075176-52076047	K562	blood:	n/a	n/a
8	RCOR1	chr19:52074190-52076188	K562	blood:	n/a	n/a
9	POLR2A	chr19:52074059-52077284	PBDE	blood:	n/a	n/a
10	SIN3AK20	chr19:52074917-52075845	K562	blood:	n/a	n/a
11	GATA1	chr19:52074810-52077148	PBDE	blood:	n/a	chr19:52075825-52075835 chr19:52074842-52074853 chr19:52076736-52076745 chr19:52076927-52076934 chr19:52076831-52076840
12	POLR2A	chr19:52074872-52077276	U87	brain:	n/a	n/a
13	POLR2A	chr19:52074900-52075262	K562	blood:	n/a	n/a
14	NFYB	chr19:52075018-52075289	GM12878	blood:	n/a	chr19:52075044-52075057
15	POLR2A	chr19:52074937-52076991	HUVEC	blood vessel:	n/a	n/a
16	RFX5	chr19:52075039-52075313	GM12878	blood:	n/a	chr19:52075147-52075161 chr19:52075150-52075159
17	POLR2A	chr19:52074893-52075358	K562	blood:	n/a	n/a
18	TEAD4	chr19:52074869-52076257	K562	blood:	n/a	n/a
19	POLR2A	chr19:52074069-52077434	U87	brain:	n/a	n/a
20	POLR2A	chr19:52074872-52077594	U87	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:51843178..51845619-chr19:52074404..52075904,2	K562	blood:
2	chr19:52073774..52076492-chr19:52083212..52084974,2	K562	blood:
3	chr19:52073066..52077206-chr19:52096074..52099799,4	K562	blood:

Variant related genes	Relation type
ZNF175	TF binding region
ENSG00000186806	Chromatin interaction
ENSG00000269388	Chromatin interaction
ENSG00000167765	Chromatin interaction
ENSG00000105497	Chromatin interaction
ENSG00000267905	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs3752128	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3752130	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3752131	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs57219903	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs57275571	1.00[ASN][1000 genomes]
rs57446594	1.00[AMR][1000 genomes]
rs57867319	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs57897206	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs58124117	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs58356296	1.00[AMR][1000 genomes]
rs58362329	1.00[ASN][1000 genomes]
rs58736474	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs58737585	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs58758423	1.00[AMR][1000 genomes]
rs58839528	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59361053	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59382174	1.00[ASN][1000 genomes]
rs59518378	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60143674	1.00[ASN][1000 genomes]
rs60314341	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60351338	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60458262	1.00[AMR][1000 genomes]
rs60618267	1.00[AMR][1000 genomes]
rs61117584	1.00[ASN][1000 genomes]
rs61235925	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61350519	1.00[ASN][1000 genomes]
rs61489792	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61511733	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61553708	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61656439	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1066308	chr19:51680133-52103974	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv544049	chr19:51680133-52103974	Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
3	nsv544051	chr19:51944903-52147459	Bivalent Enhancer Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	esv2758504	chr19:51991896-52266700	Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	542 gene(s)	inside rSNPs	diseases
5	esv2758767	chr19:51991896-52604625	Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	578 gene(s)	inside rSNPs	diseases
6	nsv469584	chr19:52001381-52151821	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
7	nsv482654	chr19:52001381-52151821	Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats 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	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52073800-52075400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
2	chr19:52073800-52075800	Active TSS	A549	lung
3	chr19:52074000-52075400	Active TSS	iPS-20b Cell Line	embryonic stem cell
4	chr19:52074000-52075400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr19:52074000-52075600	Active TSS	HUES48 Cell Line	embryonic stem cell
6	chr19:52074000-52075600	Active TSS	HUES6 Cell Line	embryonic stem cell
7	chr19:52074000-52075800	Active TSS	Rectal Mucosa Donor 29	rectum
8	chr19:52074000-52075800	Active TSS	K562	blood
9	chr19:52074000-52076000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr19:52074200-52075400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr19:52074200-52075400	Active TSS	iPS-18 Cell Line	embryonic stem cell
12	chr19:52074200-52075400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
13	chr19:52074200-52075400	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
14	chr19:52074200-52075400	Active TSS	GM12878-XiMat	blood
15	chr19:52074200-52075600	Active TSS	ES-I3 Cell Line	embryonic stem cell
16	chr19:52074200-52075600	Active TSS	H1 Cell Line	embryonic stem cell
17	chr19:52074200-52075600	Active TSS	HUES64 Cell Line	embryonic stem cell
18	chr19:52074200-52075600	Active TSS	HSMMtube	muscle
19	chr19:52074200-52075800	Active TSS	iPS-15b Cell Line	embryonic stem cell
20	chr19:52074400-52075400	Active TSS	H9 Cell Line	embryonic stem cell
21	chr19:52074400-52075400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr19:52074400-52075400	Active TSS	Colonic Mucosa	Colon
23	chr19:52074600-52075400	Active TSS	Stomach Mucosa	stomach
24	chr19:52074600-52075600	Flanking Active TSS	Primary B cells from cord blood	blood
25	chr19:52074600-52075600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
26	chr19:52074600-52075600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
27	chr19:52074600-52075800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr19:52074800-52075400	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr19:52074800-52075400	Enhancers	Primary neutrophils fromperipheralblood	blood
30	chr19:52074800-52075400	Flanking Active TSS	Primary hematopoietic stem cells	blood
31	chr19:52074800-52075400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
32	chr19:52074800-52075400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
33	chr19:52074800-52075400	Flanking Active TSS	Fetal Muscle Leg	muscle
34	chr19:52074800-52075600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
35	chr19:52074800-52075600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
36	chr19:52074800-52075600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
37	chr19:52074800-52075600	Flanking Active TSS	Thymus	Thymus
38	chr19:52074800-52075800	Flanking Active TSS	Adipose Nuclei	Adipose
39	chr19:52074800-52075800	Flanking Active TSS	Liver	Liver
40	chr19:52074800-52075800	Flanking Active TSS	Rectal Smooth Muscle	rectum
41	chr19:52074800-52076000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr19:52074800-52076000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr19:52074800-52076000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
44	chr19:52074800-52077400	Flanking Active TSS	HUVEC	blood vessel
45	chr19:52075000-52075400	Flanking Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr19:52075000-52075400	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr19:52075000-52075400	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
48	chr19:52075000-52075400	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr19:52075000-52075400	Flanking Active TSS	Primary T cells from cord blood	blood
50	chr19:52075000-52075400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood

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