Variant report

Variant	rs1654551
Chromosome Location	chr19:51412668-51412669
allele	G/T
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	JUND	chr19:51412641-51412892	K562	blood:	n/a	n/a
2	SP1	chr19:51412427-51412977	K562	blood:	n/a	chr19:51412911-51412922 chr19:51412834-51412845 chr19:51412458-51412467 chr19:51412457-51412466 chr19:51412456-51412468 chr19:51412476-51412490 chr19:51412457-51412466 chr19:51412456-51412468 chr19:51412457-51412467 chr19:51412457-51412467 chr19:51412482-51412492
3	HMGN3	chr19:51412579-51412866	K562	blood:	n/a	n/a
4	ZBTB7A	chr19:51412619-51412978	K562	blood:	n/a	n/a
5	SP4	chr19:51412444-51413137	H1-hESC	embryonic stem cell:	n/a	chr19:51412911-51412922 chr19:51412456-51412472 chr19:51412834-51412845 chr19:51412454-51412470
6	CCNT2	chr19:51412551-51412896	K562	blood:	n/a	n/a
7	IRF1	chr19:51412522-51413119	K562	blood:	n/a	n/a
8	MAZ	chr19:51412582-51413191	K562	blood:	n/a	n/a
9	TAF1	chr19:51412399-51412753	H1-hESC	embryonic stem cell:	n/a	n/a
10	SP1	chr19:51412375-51413369	H1-hESC	embryonic stem cell:	n/a	chr19:51412911-51412922 chr19:51412834-51412845 chr19:51412458-51412467 chr19:51412457-51412466 chr19:51412456-51412468 chr19:51412476-51412490 chr19:51412457-51412466 chr19:51412456-51412468 chr19:51412457-51412467 chr19:51412457-51412467 chr19:51412482-51412492
11	SP4	chr19:51412535-51413274	H1-hESC	embryonic stem cell:	n/a	chr19:51412911-51412922 chr19:51412834-51412845
12	POLR2A	chr19:51412494-51412677	H1-hESC	embryonic stem cell:	n/a	n/a
13	ELF1	chr19:51412479-51412981	K562	blood:	n/a	n/a
14	SIN3A	chr19:51412485-51412794	H1-hESC	embryonic stem cell:	n/a	n/a
15	MAX	chr19:51412544-51412909	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:51306023..51307815-chr19:51411885..51414130,3	K562	blood:
2	chr19:51305909..51308309-chr19:51411302..51414101,3	MCF-7	breast:
3	chr19:51398902..51402347-chr19:51410482..51413710,3	K562	blood:
4	chr19:51306828..51309257-chr19:51411309..51414080,2	MCF-7	breast:
5	chr19:51295380..51297114-chr19:51411572..51413706,2	K562	blood:
6	chr19:51159603..51162470-chr19:51410847..51412748,2	K562	blood:
7	chr19:51287088..51289490-chr19:51410149..51412690,2	MCF-7	breast:
8	chr19:51357203..51359934-chr19:51411354..51413552,2	K562	blood:

Variant related genes	Relation type
KLK4	TF binding region
ENSG00000197588	Chromatin interaction
ENSG00000235034	Chromatin interaction
ENSG00000268375	Chromatin interaction
ENSG00000167747	Chromatin interaction
ENSG00000261341	Chromatin interaction
ENSG00000142515	Chromatin interaction

Extended variants
information (count: 4 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs2242670	1.00[JPT][hapmap]
rs2979452	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1060760	chr19:50883425-51463712	ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
2	nsv1058177	chr19:50984774-51463712	Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:51410800-51418400	Weak transcription	Right Atrium	heart
2	chr19:51411200-51412800	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr19:51411800-51413400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
4	chr19:51412200-51412800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr19:51412200-51412800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
6	chr19:51412200-51413200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
7	chr19:51412200-51413200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
8	chr19:51412200-51413200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
9	chr19:51412200-51413400	Active TSS	H9 Cell Line	embryonic stem cell
10	chr19:51412200-51413600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
11	chr19:51412200-51413600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
12	chr19:51412200-51413600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
13	chr19:51412200-51414000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
14	chr19:51412400-51412800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr19:51412400-51412800	Flanking Bivalent TSS/Enh	Breast Myoepithelial Primary Cells	Breast
16	chr19:51412400-51412800	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr19:51412400-51412800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr19:51412400-51412800	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr19:51412400-51412800	Flanking Bivalent TSS/Enh	Brain Cingulate Gyrus	brain
20	chr19:51412400-51412800	Bivalent/Poised TSS	Brain Germinal Matrix	brain
21	chr19:51412400-51412800	Bivalent Enhancer	Colon Smooth Muscle	Colon
22	chr19:51412400-51412800	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
23	chr19:51412400-51412800	Enhancers	Pancreas	Pancrea
24	chr19:51412400-51412800	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
25	chr19:51412400-51413000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
26	chr19:51412400-51413200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
27	chr19:51412400-51413200	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
28	chr19:51412400-51413200	Bivalent Enhancer	Fetal Brain Male	brain
29	chr19:51412400-51413400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr19:51412400-51413400	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
31	chr19:51412600-51412800	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
32	chr19:51412600-51412800	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
33	chr19:51412600-51412800	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
34	chr19:51412600-51412800	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
35	chr19:51412600-51412800	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
36	chr19:51412600-51412800	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
37	chr19:51412600-51412800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr19:51412600-51412800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr19:51412600-51412800	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr19:51412600-51412800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr19:51412600-51412800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr19:51412600-51412800	Bivalent Enhancer	Adipose Nuclei	Adipose
43	chr19:51412600-51412800	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
44	chr19:51412600-51412800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
45	chr19:51412600-51412800	Bivalent Enhancer	Fetal Muscle Leg	muscle
46	chr19:51412600-51412800	Bivalent Enhancer	Fetal Stomach	stomach
47	chr19:51412600-51412800	Bivalent Enhancer	Lung	lung
48	chr19:51412600-51412800	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
49	chr19:51412600-51412800	Flanking Bivalent TSS/Enh	Right Ventricle	heart
50	chr19:51412600-51412800	Bivalent Enhancer	Thymus	Thymus

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