Variant report

Variant	rs3752131
Chromosome Location	chr19:52074571-52074572
allele	A/G
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	SIN3AK20	chr19:52074338-52074639	PFSK-1	brain:	n/a	n/a
2	POLR2A	chr19:52074406-52074752	HepG2	liver:	n/a	n/a
3	ATF2	chr19:52074106-52074660	GM12878	blood:	n/a	n/a
4	SPI1	chr19:52074389-52074614	K562	blood:	n/a	chr19:52074513-52074526
5	POLR2A	chr19:52074428-52074658	GM12878	blood:	n/a	n/a
6	TEAD4	chr19:52074238-52074685	HepG2	liver:	n/a	chr19:52074268-52074277
7	YY1	chr19:52073915-52074690	GM12892	blood:	n/a	chr19:52074309-52074321
8	GTF2F1	chr19:52074274-52074578	K562	blood:	n/a	n/a
9	MYC	chr19:52074217-52074615	MCF10A-Er-Src	breast:	n/a	n/a
10	GABPA	chr19:52074258-52074894	HL-60	blood:	n/a	chr19:52074457-52074471 chr19:52074460-52074474 chr19:52074460-52074471
11	POLR2A	chr19:52074162-52074835	K562	blood:	n/a	n/a
12	RFX5	chr19:52074286-52074680	GM12878	blood:	n/a	n/a
13	PML	chr19:52074172-52074760	K562	blood:	n/a	n/a
14	TBP	chr19:52074094-52074697	K562	blood:	n/a	n/a
15	FOXM1	chr19:52074189-52074713	GM12878	blood:	n/a	n/a
16	POLR2A	chr19:52074297-52074786	PANC-1	pancreas:	n/a	n/a
17	HEY1	chr19:52074361-52074728	HepG2	liver:	n/a	n/a
18	TBL1XR1	chr19:52074185-52074610	GM12878	blood:	n/a	n/a
19	RCOR1	chr19:52074083-52074616	GM12878	blood:	n/a	n/a
20	RELA	chr19:52074187-52074749	GM19099	blood:	n/a	n/a
21	SIX5	chr19:52074067-52074819	A549	lung:	n/a	n/a
22	MAX	chr19:52074185-52074682	K562	blood:	n/a	n/a
23	POLR2A	chr19:52074326-52074714	Hela-S3	cervix:	n/a	n/a
24	POLR2A	chr19:52074396-52074814	HUVEC	blood vessel:	n/a	n/a
25	BCL3	chr19:52074184-52074769	A549	lung:	n/a	chr19:52074479-52074487 chr19:52074517-52074526
26	POLR2A	chr19:52074425-52074677	HepG2	liver:	n/a	n/a
27	PML	chr19:52074274-52074608	GM12878	blood:	n/a	n/a
28	YY1	chr19:52074019-52074684	HepG2	liver:	n/a	chr19:52074309-52074321
29	TEAD4	chr19:52074320-52074774	ECC-1	luminal epithelium:	n/a	n/a
30	MAX	chr19:52074074-52074932	A549	lung:	n/a	n/a
31	ETS1	chr19:52074077-52074712	A549	lung:	n/a	chr19:52074516-52074525 chr19:52074513-52074529 chr19:52074517-52074526 chr19:52074515-52074524 chr19:52074517-52074526 chr19:52074518-52074528 chr19:52074517-52074528 chr19:52074517-52074526 chr19:52074514-52074527 chr19:52074517-52074526 chr19:52074517-52074526 chr19:52074517-52074526 chr19:52074517-52074526
32	YY1	chr19:52073950-52074902	SK-N-SH	brain:	n/a	chr19:52074309-52074321
33	YY1	chr19:52073863-52074823	A549	lung:	n/a	chr19:52074309-52074321
34	POLR2A	chr19:52074439-52074663	A549	lung:	n/a	n/a
35	HEY1	chr19:52074151-52074648	K562	blood:	n/a	n/a
36	POLR2A	chr19:52074470-52074646	HepG2	liver:	n/a	n/a
37	MAFK	chr19:52074105-52074641	K562	blood:	n/a	n/a
38	ELK1	chr19:52074128-52074673	K562	blood:	n/a	chr19:52074517-52074526 chr19:52074517-52074526
39	SETDB1	chr19:52074250-52074591	U2OS	brain:	n/a	n/a
40	CREB1	chr19:52074176-52074734	K562	blood:	n/a	n/a
41	MYC	chr19:52074214-52074614	MCF10A-Er-Src	breast:	n/a	n/a
42	NR2F2	chr19:52074045-52075159	K562	blood:	n/a	n/a
43	NRF1	chr19:52074363-52074591	HepG2	liver:	n/a	chr19:52074457-52074471 chr19:52074459-52074470 chr19:52074460-52074474 chr19:52074460-52074471
44	CHD1	chr19:52074193-52074853	GM12878	blood:	n/a	n/a
45	ELF1	chr19:52074212-52074792	K562	blood:	n/a	chr19:52074516-52074525 chr19:52074513-52074526 chr19:52074515-52074526 chr19:52074515-52074526
46	BRCA1	chr19:52074249-52074643	GM12878	blood:	n/a	chr19:52074547-52074554
47	USF1	chr19:52074152-52074754	A549	lung:	n/a	n/a
48	SIX5	chr19:52074149-52074673	GM12878	blood:	n/a	n/a
49	SIX5	chr19:52073945-52074824	A549	lung:	n/a	n/a
50	THAP1	chr19:52074239-52074683	K562	blood:	n/a	chr19:52074416-52074440

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
ENSG00000167765	Chromatin interaction
ENSG00000186806	Chromatin interaction
ENSG00000269388	Chromatin interaction
ENSG00000267905	Chromatin interaction
ENSG00000105497	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]
rs56937816	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:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52073800-52075000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr19:52073800-52075000	Active TSS	Brain Inferior Temporal Lobe	brain
3	chr19:52073800-52075200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr19:52073800-52075400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
5	chr19:52073800-52075800	Active TSS	A549	lung
6	chr19:52074000-52074600	Active TSS	Primary B cells from cord blood	blood
7	chr19:52074000-52074600	Active TSS	Primary T regulatory cells fromperipheralblood	blood
8	chr19:52074000-52074600	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
9	chr19:52074000-52074800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
10	chr19:52074000-52074800	Active TSS	Primary hematopoietic stem cells	blood
11	chr19:52074000-52074800	Active TSS	Cortex derived primary cultured neurospheres	brain
12	chr19:52074000-52074800	Active TSS	Adipose Nuclei	Adipose
13	chr19:52074000-52074800	Active TSS	Liver	Liver
14	chr19:52074000-52074800	Active TSS	Thymus	Thymus
15	chr19:52074000-52074800	Active TSS	Monocytes-CD14+_RO01746	blood
16	chr19:52074000-52075000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr19:52074000-52075000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
18	chr19:52074000-52075000	Active TSS	Primary hematopoietic stem cells short term culture	blood
19	chr19:52074000-52075000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr19:52074000-52075000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr19:52074000-52075000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr19:52074000-52075000	Active TSS	Brain Anterior Caudate	brain
23	chr19:52074000-52075000	Active TSS	Brain Cingulate Gyrus	brain
24	chr19:52074000-52075000	Active TSS	Brain Hippocampus Middle	brain
25	chr19:52074000-52075000	Active TSS	Duodenum Smooth Muscle	Duodenum
26	chr19:52074000-52075000	Active TSS	Fetal Brain Female	brain
27	chr19:52074000-52075000	Active TSS	Hela-S3	cervix
28	chr19:52074000-52075000	Active TSS	HMEC	breast
29	chr19:52074000-52075000	Active TSS	NHLF	lung
30	chr19:52074000-52075200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr19:52074000-52075200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr19:52074000-52075200	Active TSS	Muscle Satellite Cultured Cells	--
33	chr19:52074000-52075200	Active TSS	Brain Germinal Matrix	brain
34	chr19:52074000-52075200	Active TSS	NHDF-Ad	bronchial
35	chr19:52074000-52075400	Active TSS	iPS-20b Cell Line	embryonic stem cell
36	chr19:52074000-52075400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr19:52074000-52075600	Active TSS	HUES48 Cell Line	embryonic stem cell
38	chr19:52074000-52075600	Active TSS	HUES6 Cell Line	embryonic stem cell
39	chr19:52074000-52075800	Active TSS	Rectal Mucosa Donor 29	rectum
40	chr19:52074000-52075800	Active TSS	K562	blood
41	chr19:52074000-52076000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr19:52074200-52074600	Active TSS	Primary T helper cells PMA-I stimulated	--
43	chr19:52074200-52074600	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr19:52074200-52074600	Active TSS	Skeletal Muscle Female	skeletal muscle
45	chr19:52074200-52074800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr19:52074200-52074800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr19:52074200-52074800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
48	chr19:52074200-52074800	Active TSS	Primary T killer memory cells from peripheral blood	blood
49	chr19:52074200-52074800	Active TSS	Fetal Muscle Leg	muscle
50	chr19:52074200-52074800	Active TSS	Rectal Smooth Muscle	rectum

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