Variant report

Variant	rs28384479
Chromosome Location	chr19:38865586-38865587
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:463)
CpG islands
(count:0)
Chromatin interactive
region (count:23)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:463 , 50 per page) page: 1 2 3 4 5 6 7 ... 10

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	REST	chr19:38865240-38865679	HepG2	liver:	n/a	n/a
2	PBX3	chr19:38864781-38865840	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr19:38864824-38865795	NB4	blood:	n/a	n/a
4	ELF1	chr19:38864753-38865795	A549	lung:	n/a	n/a
5	POLR2A	chr19:38864872-38865834	HepG2	liver:	n/a	n/a
6	REST	chr19:38865252-38865602	PFSK-1	brain:	n/a	n/a
7	POLR2A	chr19:38864888-38865886	GM12878	blood:	n/a	n/a
8	FOXP2	chr19:38864964-38865722	PFSK-1	brain:	n/a	n/a
9	JUND	chr19:38864814-38866038	K562	blood:	n/a	n/a
10	CREB1	chr19:38864879-38865850	A549	lung:	n/a	n/a
11	POLR2A	chr19:38864860-38865921	ECC-1	luminal epithelium:	n/a	n/a
12	PAX5	chr19:38865262-38865882	GM12878	blood:	n/a	n/a
13	CTCF	chr19:38865520-38865670	GM12878	blood:	n/a	n/a
14	CREB1	chr19:38864779-38865722	HepG2	liver:	n/a	n/a
15	RCOR1	chr19:38864867-38865662	GM12878	blood:	n/a	n/a
16	POLR2A	chr19:38864822-38865813	HUVEC	blood vessel:	n/a	n/a
17	POLR2A	chr19:38864672-38866574	PBDE	blood:	n/a	n/a
18	TAF1	chr19:38864910-38865712	Hela-S3	cervix:	n/a	n/a
19	YY1	chr19:38864825-38865945	GM12892	blood:	n/a	chr19:38865199-38865215 chr19:38865108-38865130 chr19:38865200-38865222
20	SIN3A	chr19:38864887-38866093	H1-hESC	embryonic stem cell:	n/a	n/a
21	HMGN3	chr19:38864989-38865873	K562	blood:	n/a	n/a
22	POLR2A	chr19:38864836-38865642	K562	blood:	n/a	n/a
23	POLR2A	chr19:38864697-38866015	GM12892	blood:	n/a	n/a
24	POLR2A	chr19:38864793-38865860	GM12878	blood:	n/a	n/a
25	PML	chr19:38864806-38865683	GM12878	blood:	n/a	n/a
26	RAD21	chr19:38864834-38866138	A549	lung:	n/a	n/a
27	ELK1	chr19:38864921-38865705	K562	blood:	n/a	chr19:38865192-38865201 chr19:38865192-38865201
28	TAF1	chr19:38865152-38865752	PFSK-1	brain:	n/a	n/a
29	MAX	chr19:38864380-38866330	A549	lung:	n/a	n/a
30	TAF1	chr19:38864972-38865912	GM12892	blood:	n/a	n/a
31	POLR2A	chr19:38864797-38865697	U87	brain:	n/a	n/a
32	MXI1	chr19:38864901-38865831	HepG2	liver:	n/a	n/a
33	STAT5A	chr19:38864788-38866263	GM12878	blood:	n/a	chr19:38865795-38865807
34	FOSL2	chr19:38864904-38865609	HepG2	liver:	n/a	n/a
35	YY1	chr19:38864854-38865711	GM12891	blood:	n/a	chr19:38865199-38865215 chr19:38865108-38865130 chr19:38865200-38865222
36	POLR2A	chr19:38865237-38865854	A549	lung:	n/a	n/a
37	MAZ	chr19:38864932-38865650	Hela-S3	cervix:	n/a	n/a
38	CUX1	chr19:38864715-38865599	GM12878	blood:	n/a	chr19:38865116-38865127
39	CTCF	chr19:38865500-38865650	HEK293	kidney:	n/a	n/a
40	ATF3	chr19:38864686-38866133	A549	lung:	n/a	n/a
41	RCOR1	chr19:38864925-38865650	K562	blood:	n/a	n/a
42	POLR2A	chr19:38864810-38865882	GM12892	blood:	n/a	n/a
43	RELA	chr19:38864802-38866110	GM15510	blood:	n/a	n/a
44	BCLAF1	chr19:38864827-38865772	GM12878	blood:	n/a	chr19:38865192-38865201
45	POLR2A	chr19:38864880-38865731	HUVEC	blood vessel:	n/a	n/a
46	NR2F2	chr19:38864842-38866310	K562	blood:	n/a	n/a
47	EP300	chr19:38864671-38865792	K562	blood:	n/a	chr19:38865193-38865200
48	PBX3	chr19:38864819-38865654	SK-N-SH	brain:	n/a	n/a
49	MXI1	chr19:38864955-38865611	H1-hESC	embryonic stem cell:	n/a	n/a
50	MAX	chr19:38864899-38865652	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:23 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:38839437..38845026-chr19:38862738..38867726,6	MCF-7	breast:
2	chr19:38824024..38830842-chr19:38863522..38868048,10	MCF-7	breast:
3	chr19:38864536..38866994-chr19:38891927..38895682,4	MCF-7	breast:
4	chr19:38824766..38830853-chr19:38863348..38868089,16	MCF-7	breast:
5	chr19:38851019..38853857-chr19:38863435..38867110,13	MCF-7	breast:
6	chr19:38704545..38706333-chr19:38863890..38866208,2	K562	blood:
7	chr19:38850348..38855103-chr19:38862504..38867180,11	K562	blood:
8	chr19:38753811..38757692-chr19:38863788..38867160,7	MCF-7	breast:
9	chr19:38806279..38807928-chr19:38863720..38866328,2	K562	blood:
10	chr1:108742828..108743565-chr19:38865046..38865778,2	Hela-S3	cervix:
11	chr19:38747172..38749523-chr19:38863877..38866599,2	K562	blood:
12	chr19:38849999..38854779-chr19:38863669..38868606,10	K562	blood:
13	chr19:38864731..38867116-chr19:38892888..38894994,2	MCF-7	breast:
14	chr19:38713237..38716742-chr19:38865084..38866886,4	MCF-7	breast:
15	chr19:38865264..38867147-chr19:38906342..38908608,2	MCF-7	breast:
16	chr19:38823410..38828693-chr19:38863569..38867873,9	K562	blood:
17	chr19:38865210..38867100-chr19:38887808..38889837,2	MCF-7	breast:
18	chr19:38825004..38828693-chr19:38863595..38867873,9	K562	blood:
19	chr19:38810865..38812439-chr19:38865172..38866719,2	MCF-7	breast:
20	chr19:38865462..38867810-chr19:38887445..38890114,2	K562	blood:
21	chr19:38851531..38855576-chr19:38863499..38866575,5	MCF-7	breast:
22	chr19:38711690..38716111-chr19:38864242..38867673,4	MCF-7	breast:
23	chr19:38718989..38720789-chr19:38865301..38866855,2	MCF-7	breast:

No data

Variant related genes	Relation type
PSMD8	TF binding region
ENSG00000099338	Chromatin interaction
ENSG00000171777	Chromatin interaction
ENSG00000099337	Chromatin interaction
ENSG00000130244	Chromatin interaction
ENSG00000238838	Chromatin interaction
ENSG00000167641	Chromatin interaction
ENSG00000267473	Chromatin interaction
ENSG00000167642	Chromatin interaction
ENSG00000167645	Chromatin interaction
ENSG00000011332	Chromatin interaction
ENSG00000266963	Chromatin interaction
ENSG00000085491	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs2302228	1.00[ASN][1000 genomes]
rs3745963	0.85[ASN][1000 genomes]
rs3760884	1.00[ASN][1000 genomes]
rs57753437	0.85[ASN][1000 genomes]
rs59491640	0.85[ASN][1000 genomes]
rs60780508	0.85[ASN][1000 genomes]
rs73043027	0.82[ASN][1000 genomes]
rs73044947	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063471	chr19:38734744-39148392	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	73 gene(s)	inside rSNPs	diseases
2	nsv833822	chr19:38760748-38945105	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
3	nsv911658	chr19:38785318-39002140	Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
4	nsv470140	chr19:38840139-39119494	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
5	nsv911659	chr19:38852357-39002140	Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
6	nsv911660	chr19:38852357-39060238	Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Strong transcription Weak transcription Genic 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	41 gene(s)	inside rSNPs	diseases
7	nsv833823	chr19:38855550-39035800	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
8	nsv1064275	chr19:38859865-38913251	Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38864000-38866800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr19:38864400-38866200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr19:38864600-38865800	Active TSS	Liver	Liver
4	chr19:38864600-38865800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
5	chr19:38864600-38866000	Active TSS	Brain Substantia Nigra	brain
6	chr19:38864600-38866000	Active TSS	Duodenum Smooth Muscle	Duodenum
7	chr19:38864600-38866000	Active TSS	Rectal Smooth Muscle	rectum
8	chr19:38864600-38866000	Active TSS	Thymus	Thymus
9	chr19:38864600-38866200	Active TSS	HUES64 Cell Line	embryonic stem cell
10	chr19:38864600-38866200	Active TSS	Breast Myoepithelial Primary Cells	Breast
11	chr19:38864600-38866200	Active TSS	Colon Smooth Muscle	Colon
12	chr19:38864600-38866200	Active TSS	Fetal Kidney	kidney
13	chr19:38864600-38866200	Active TSS	Fetal Lung	lung
14	chr19:38864600-38866200	Active TSS	GM12878-XiMat	blood
15	chr19:38864600-38866200	Active TSS	Hela-S3	cervix
16	chr19:38864600-38866400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr19:38864600-38866400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr19:38864600-38866400	Active TSS	Fetal Intestine Large	intestine
19	chr19:38864600-38866800	Active TSS	HUES48 Cell Line	embryonic stem cell
20	chr19:38864600-38866800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr19:38864600-38866800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr19:38864600-38867000	Active TSS	ES-I3 Cell Line	embryonic stem cell
23	chr19:38864600-38867000	Active TSS	H9 Cell Line	embryonic stem cell
24	chr19:38864600-38867000	Active TSS	Pancreatic Islets	Pancreatic Islet
25	chr19:38864800-38865800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr19:38864800-38865800	Active TSS	Primary B cells from cord blood	blood
27	chr19:38864800-38865800	Active TSS	Primary T regulatory cells fromperipheralblood	blood
28	chr19:38864800-38865800	Active TSS	Brain Cingulate Gyrus	brain
29	chr19:38864800-38865800	Active TSS	Brain Germinal Matrix	brain
30	chr19:38864800-38865800	Active TSS	Colonic Mucosa	Colon
31	chr19:38864800-38866000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr19:38864800-38866000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr19:38864800-38866000	Active TSS	Primary T killer memory cells from peripheral blood	blood
34	chr19:38864800-38866000	Active TSS	Brain Angular Gyrus	brain
35	chr19:38864800-38866000	Active TSS	Brain Hippocampus Middle	brain
36	chr19:38864800-38866000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
37	chr19:38864800-38866000	Active TSS	Fetal Brain Female	brain
38	chr19:38864800-38866000	Active TSS	Fetal Muscle Leg	muscle
39	chr19:38864800-38866000	Active TSS	Fetal Stomach	stomach
40	chr19:38864800-38866000	Active TSS	Pancreas	Pancrea
41	chr19:38864800-38866000	Active TSS	Placenta Amnion	Placenta Amnion
42	chr19:38864800-38866000	Active TSS	Right Ventricle	heart
43	chr19:38864800-38866000	Active TSS	Stomach Mucosa	stomach
44	chr19:38864800-38866200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr19:38864800-38866200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr19:38864800-38866200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr19:38864800-38866200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr19:38864800-38866200	Active TSS	Brain Inferior Temporal Lobe	brain
49	chr19:38864800-38866200	Active TSS	Esophagus	oesophagus
50	chr19:38864800-38866200	Active TSS	Fetal Intestine Small	intestine

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