Variant report

Variant	rs390784
Chromosome Location	chr19:44488189-44488190
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:257)
CpG islands
(count:122)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:257 , 50 per page) page: 1 2 3 4 5 6

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BRCA1	chr19:44488118-44488890	H1-hESC	embryonic stem cell:	n/a	n/a
2	GABPA	chr19:44488167-44488455	K562	blood:	n/a	n/a
3	SIX5	chr19:44487940-44488616	A549	lung:	n/a	n/a
4	REST	chr19:44488077-44488308	K562	blood:	n/a	n/a
5	POLR2A	chr19:44488081-44488834	GM12891	blood:	n/a	n/a
6	CEBPB	chr19:44488141-44488905	H1-hESC	embryonic stem cell:	n/a	n/a
7	BCLAF1	chr19:44488019-44488497	GM12878	blood:	n/a	chr19:44488345-44488354
8	MXI1	chr19:44487660-44489009	GM12878	blood:	n/a	n/a
9	RFX5	chr19:44488128-44488292	HepG2	liver:	n/a	n/a
10	CEBPB	chr19:44488033-44488905	Hela-S3	cervix:	n/a	n/a
11	SPI1	chr19:44488145-44488338	K562	blood:	n/a	n/a
12	MAZ	chr19:44488101-44488379	K562	blood:	n/a	n/a
13	FOXP2	chr19:44488063-44488410	SK-N-MC	brain:	n/a	n/a
14	CREB1	chr19:44488042-44488578	H1-hESC	embryonic stem cell:	n/a	n/a
15	TBP	chr19:44487854-44488809	GM12878	blood:	n/a	n/a
16	BHLHE40	chr19:44488086-44488370	K562	blood:	n/a	n/a
17	POLR2A	chr19:44488062-44488476	HUVEC	blood vessel:	n/a	n/a
18	MAX	chr19:44488030-44488443	H1-hESC	embryonic stem cell:	n/a	n/a
19	MAX	chr19:44488002-44488560	Hela-S3	cervix:	n/a	n/a
20	NFIC	chr19:44488038-44488574	SK-N-SH	brain:	n/a	n/a
21	ELF1	chr19:44487936-44488697	HCT-116	colon:	n/a	chr19:44488344-44488357 chr19:44488345-44488356 chr19:44488345-44488356
22	TAF1	chr19:44488096-44488493	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr19:44488027-44488668	GM12878	blood:	n/a	n/a
24	ELF1	chr19:44488006-44488719	GM12878	blood:	n/a	chr19:44488344-44488357 chr19:44488345-44488356 chr19:44488345-44488356
25	TAF1	chr19:44488184-44488519	SK-N-SH	brain:	n/a	n/a
26	MYC	chr19:44488103-44488458	K562	blood:	n/a	n/a
27	MAFK	chr19:44488155-44488347	HepG2	liver:	n/a	n/a
28	YY1	chr19:44488026-44488495	GM12891	blood:	n/a	n/a
29	NFIC	chr19:44487881-44488663	ECC-1	luminal epithelium:	n/a	n/a
30	MAX	chr19:44488092-44488378	K562	blood:	n/a	n/a
31	SIX5	chr19:44488049-44488433	K562	blood:	n/a	n/a
32	YY1	chr19:44487996-44488455	HepG2	liver:	n/a	n/a
33	GABPA	chr19:44487808-44488816	MCF-7	breast:	n/a	chr19:44488607-44488616
34	POLR2A	chr19:44488061-44488566	SK-N-MC	brain:	n/a	n/a
35	STAT3	chr19:44488107-44488378	MCF10A-Er-Src	breast:	n/a	chr19:44488233-44488244
36	ELF1	chr19:44488073-44488570	K562	blood:	n/a	chr19:44488344-44488357 chr19:44488345-44488356 chr19:44488345-44488356
37	MYBL2	chr19:44488038-44488552	HepG2	liver:	n/a	n/a
38	CEBPB	chr19:44488140-44488931	IMR90	lung:	n/a	n/a
39	CREB1	chr19:44488015-44488551	HepG2	liver:	n/a	n/a
40	POLR2A	chr19:44488061-44488609	GM12892	blood:	n/a	n/a
41	YY1	chr19:44488079-44488398	HepG2	liver:	n/a	n/a
42	MAFK	chr19:44488106-44488441	IMR90	lung:	n/a	n/a
43	GTF2F1	chr19:44488035-44488472	Hela-S3	cervix:	n/a	n/a
44	GABPA	chr19:44487970-44488656	A549	lung:	n/a	chr19:44488607-44488616
45	POLR2A	chr19:44488097-44488587	H1-hESC	embryonic stem cell:	n/a	n/a
46	YY1	chr19:44488126-44488374	K562	blood:	n/a	n/a
47	ZNF143	chr19:44487920-44488592	H1-hESC	embryonic stem cell:	n/a	n/a
48	STAT3	chr19:44488151-44488349	MCF10A-Er-Src	breast:	n/a	chr19:44488233-44488244
49	ZNF143	chr19:44487950-44488503	K562	blood:	n/a	n/a
50	BHLHE40	chr19:44487743-44488977	GM12878	blood:	n/a	n/a

(count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:44488170-44488220	SK-N-SH	brain:	n/a
2	chr19:44488181-44488231	AG04449	skin:	fetal
3	chr19:44488170-44488220	T-47D	breast:	n/a
4	chr19:44488170-44488220	AG09319	gingival:	n/a
5	chr19:44488170-44488220	AG04450	lung:	fetal
6	chr19:44488181-44488231	HRCEpiC	kidney:	n/a
7	chr19:44488181-44488231	HUVEC	blood vessel:	n/a
8	chr19:44488170-44488220	GM06990	blood:	n/a
9	chr19:44488181-44488231	HCM	heart:	n/a
10	chr19:44488181-44488231	HepG2	liver:	n/a
11	chr19:44488181-44488231	SAEC	small airway:	n/a
12	chr19:44488181-44488231	NT2-D1	testis:	n/a
13	chr19:44488181-44488231	U87	brain:	n/a
14	chr19:44488181-44488231	BJ	skin:	n/a
15	chr19:44488170-44488220	HRPEpiC	eye:	n/a
16	chr19:44488170-44488220	HRE	kidney:	n/a
17	chr19:44488170-44488220	GM19239	blood:	n/a
18	chr19:44488170-44488220	CMK	blood:	n/a
19	chr19:44488181-44488231	SK-N-SH	brain:	n/a
20	chr19:44488170-44488220	HIPEpiC	eye:	n/a
21	chr19:44488170-44488220	HRCEpiC	kidney:	n/a
22	chr19:44488181-44488231	HPAEpiC	pulmonary alveolar:	n/a
23	chr19:44488181-44488231	LNCaP	prostate:	n/a
24	chr19:44488181-44488231	Caco-2	colon:	n/a
25	chr19:44488181-44488231	HEK293	kidney:	embryo
26	chr19:44488181-44488231	GM06990	blood:	n/a
27	chr19:44488181-44488231	RPTEC	kidney:	n/a
28	chr19:44488170-44488220	NHDF-neo	bronchial:	n/a
29	chr19:44488170-44488220	HAEpiC	amniotic membrane:	n/a
30	chr19:44488181-44488231	A549	lung:	n/a
31	chr19:44488181-44488231	MCF-7	breast:	n/a
32	chr19:44488170-44488220	LNCaP	prostate:	n/a
33	chr19:44488170-44488220	Caco-2	colon:	n/a
34	chr19:44488181-44488231	GM19239	blood:	n/a
35	chr19:44488181-44488231	AG10803	skin:	n/a
36	chr19:44488170-44488220	RPTEC	kidney:	n/a
37	chr19:44488170-44488220	NT2-D1	testis:	n/a
38	chr19:44488181-44488231	ovcar-3	ovarian:	n/a
39	chr19:44488170-44488220	SK-N-SH_RA	brain:	n/a
40	chr19:44488170-44488220	HMEC	breast:	n/a
41	chr19:44488181-44488231	Hepatocyte	liver:	n/a
42	chr19:44488170-44488220	AoSMC	blood vessel:	n/a
43	chr19:44488170-44488220	GM12892	blood:	n/a
44	chr19:44488170-44488220	BJ	skin:	n/a
45	chr19:44488170-44488220	HCF	heart:	n/a
46	chr19:44488170-44488220	HCM	heart:	n/a
47	chr19:44488181-44488231	AG09319	gingival:	n/a
48	chr19:44488170-44488220	NB4	blood:	n/a
49	chr19:44488170-44488220	Hela-S3	cervix:	n/a
50	chr19:44488181-44488231	CMK	blood:	n/a

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:44486769..44491037-chr19:44505585..44508395,4	MCF-7	breast:
2	chr19:44487777..44490285-chr19:44555817..44558004,3	MCF-7	breast:
3	chr19:44487658..44489792-chr19:44505545..44508358,4	MCF-7	breast:

No data

Variant related genes	Relation type
ZNF155	TF binding region
ZNF155	CpG island
ENSG00000178386	Chromatin interaction
ENSG00000266921	Chromatin interaction
ENSG00000159882	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11881642	0.86[MEX][hapmap]
rs384596	0.87[EUR][1000 genomes]
rs397706	0.85[CEU][hapmap];0.87[TSI][hapmap]
rs398981	0.85[CEU][hapmap];0.87[TSI][hapmap]
rs415499	0.96[CEU][hapmap];0.83[TSI][hapmap];0.87[EUR][1000 genomes]
rs425530	0.81[EUR][1000 genomes]
rs430746	1.00[CEU][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes]
rs55821779	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56053925	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7255894	0.81[CEU][hapmap]
rs8099924	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469650	chr19:44405994-44555426	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv579854	chr19:44411543-44490024	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv912109	chr19:44459074-44493142	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs390784	RP11-15A1.7	cis	Whole Blood	GTEx
rs390784	ZNF155	cis	Whole Blood	GTEx
rs390784	FOXA3	cis	cerebellum	SCAN
rs390784	KLK6	cis	parietal	SCAN
rs390784	PNMAL1	cis	parietal	SCAN
rs390784	ZNF528	cis	parietal	SCAN

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44485200-44488200	Weak transcription	Aorta	Aorta
2	chr19:44487600-44488200	Flanking Active TSS	Dnd41	blood
3	chr19:44487600-44488400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr19:44487600-44488800	Active TSS	Primary T helper cells fromperipheralblood	blood
5	chr19:44487600-44488800	Active TSS	Brain Anterior Caudate	brain
6	chr19:44487600-44488800	Active TSS	Rectal Smooth Muscle	rectum
7	chr19:44487600-44489200	Active TSS	Brain Cingulate Gyrus	brain
8	chr19:44487600-44489200	Active TSS	Brain Inferior Temporal Lobe	brain
9	chr19:44487600-44489200	Active TSS	Brain Substantia Nigra	brain
10	chr19:44487600-44489200	Active TSS	Psoas Muscle	Psoas
11	chr19:44487600-44489200	Active TSS	Hela-S3	cervix
12	chr19:44487600-44489400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr19:44487600-44489400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr19:44487600-44489400	Active TSS	Duodenum Mucosa	Duodenum
15	chr19:44487600-44489400	Active TSS	Rectal Mucosa Donor 29	rectum
16	chr19:44487600-44489400	Active TSS	Skeletal Muscle Male	skeletal muscle
17	chr19:44487600-44489600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr19:44487600-44489600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr19:44487600-44489600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr19:44487600-44489600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr19:44487600-44489600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr19:44487600-44489600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr19:44487800-44488200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr19:44487800-44488200	Flanking Active TSS	Primary B cells from cord blood	blood
25	chr19:44487800-44488200	Flanking Active TSS	Adipose Nuclei	Adipose
26	chr19:44487800-44488200	Weak transcription	Pancreas	Pancrea
27	chr19:44487800-44488200	Flanking Active TSS	Thymus	Thymus
28	chr19:44487800-44488200	Flanking Active TSS	HUVEC	blood vessel
29	chr19:44487800-44488200	Flanking Active TSS	NH-A	brain
30	chr19:44487800-44488400	Active TSS	Primary T regulatory cells fromperipheralblood	blood
31	chr19:44487800-44488400	Active TSS	Stomach Smooth Muscle	stomach
32	chr19:44487800-44488400	Active TSS	HepG2	liver
33	chr19:44487800-44488400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
34	chr19:44487800-44488800	Active TSS	Primary neutrophils fromperipheralblood	blood
35	chr19:44487800-44488800	Active TSS	Primary T cells from cord blood	blood
36	chr19:44487800-44488800	Active TSS	Primary hematopoietic stem cells	blood
37	chr19:44487800-44488800	Active TSS	Cortex derived primary cultured neurospheres	brain
38	chr19:44487800-44488800	Active TSS	Brain Germinal Matrix	brain
39	chr19:44487800-44488800	Active TSS	Fetal Muscle Leg	muscle
40	chr19:44487800-44489000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr19:44487800-44489000	Active TSS	Fetal Heart	heart
42	chr19:44487800-44489000	Active TSS	Placenta Amnion	Placenta Amnion
43	chr19:44487800-44489000	Active TSS	Osteobl	bone
44	chr19:44487800-44489200	Active TSS	HUES48 Cell Line	embryonic stem cell
45	chr19:44487800-44489200	Active TSS	iPS-15b Cell Line	embryonic stem cell
46	chr19:44487800-44489200	Active TSS	iPS-18 Cell Line	embryonic stem cell
47	chr19:44487800-44489200	Active TSS	Primary T helper naive cells from peripheral blood	blood
48	chr19:44487800-44489200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr19:44487800-44489200	Active TSS	Brain Angular Gyrus	brain
50	chr19:44487800-44489200	Active TSS	Brain Hippocampus Middle	brain

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