Variant report

Variant	rs2365725
Chromosome Location	chr19:55672470-55672471
allele	C/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	MAX	chr19:55671894-55672869	H1-hESC	embryonic stem cell:	n/a	n/a
2	CREB1	chr19:55671898-55672639	H1-hESC	embryonic stem cell:	n/a	n/a
3	SP4	chr19:55671842-55672609	H1-hESC	embryonic stem cell:	n/a	chr19:55672150-55672166 chr19:55672152-55672168 chr19:55672184-55672200 chr19:55672186-55672197
4	MAX	chr19:55671359-55672503	HCT-116	colon:	n/a	n/a
5	E2F6	chr19:55671853-55672895	H1-hESC	embryonic stem cell:	n/a	chr19:55672795-55672807
6	MAX	chr19:55671792-55672762	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr19:55672282-55672488	H1-hESC	embryonic stem cell:	n/a	n/a
8	TBP	chr19:55671876-55672553	H1-hESC	embryonic stem cell:	n/a	n/a
9	CTCF	chr19:55671426-55672696	A549	lung:	n/a	n/a
10	RAD21	chr19:55671663-55672478	HCT-116	colon:	n/a	chr19:55671960-55671969
11	HMGN3	chr19:55671922-55672576	K562	blood:	n/a	n/a
12	FOXP2	chr19:55671915-55672687	PFSK-1	brain:	n/a	n/a
13	CTCF	chr19:55671459-55672495	SK-N-SH	brain:	n/a	n/a
14	E2F6	chr19:55671759-55673691	H1-hESC	embryonic stem cell:	n/a	chr19:55672795-55672807 chr19:55673196-55673206
15	RAD21	chr19:55671518-55672485	HCT-116	colon:	n/a	chr19:55671960-55671969
16	POLR2A	chr19:55671851-55672715	PFSK-1	brain:	n/a	n/a
17	TAF1	chr19:55672283-55672648	PFSK-1	brain:	n/a	n/a
18	CCNT2	chr19:55671910-55672510	K562	blood:	n/a	n/a
19	SP1	chr19:55671855-55672482	H1-hESC	embryonic stem cell:	n/a	chr19:55672155-55672165 chr19:55672154-55672166 chr19:55672260-55672272 chr19:55672188-55672197 chr19:55672186-55672198 chr19:55672187-55672196 chr19:55672186-55672198 chr19:55672154-55672166 chr19:55672186-55672197 chr19:55672262-55672271 chr19:55672155-55672165 chr19:55672188-55672197
20	POLR2A	chr19:55671742-55672794	PFSK-1	brain:	n/a	n/a
21	POLR2A	chr19:55672468-55672554	MCF-7	breast:	n/a	n/a
22	POLR2A	chr19:55672370-55672490	K562	blood:	n/a	n/a
23	BACH1	chr19:55671866-55672635	H1-hESC	embryonic stem cell:	n/a	n/a
24	SMC3	chr19:55671392-55672538	SK-N-SH	brain:	n/a	n/a
25	MAZ	chr19:55671753-55672659	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:55627388..55629698-chr19:55672061..55673602,2	K562	blood:
2	chr19:55579852..55582710-chr19:55671936..55674879,2	K562	blood:
3	chr19:55657215..55657931-chr19:55671632..55672517,3	K562	blood:
4	chr19:55669904..55673815-chr19:55917688..55921815,5	K562	blood:
5	chr19:55668909..55673851-chr19:55684249..55689420,6	K562	blood:
6	chr19:55670803..55672973-chr19:55678461..55680015,2	MCF-7	breast:
7	chr19:55672196..55674741-chr19:55676544..55679173,3	K562	blood:
8	chr19:55669094..55672573-chr19:55676633..55678240,3	K562	blood:
9	chr19:55652274..55653243-chr19:55671651..55672648,4	K562	blood:
10	chr19:55657720..55659447-chr19:55670409..55672561,2	MCF-7	breast:
11	chr19:55670813..55674787-chr19:55917654..55919984,3	MCF-7	breast:
12	chr19:55656783..55658511-chr19:55670096..55672623,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-EPS8L1-2	chr19:55672414-55672582	ENSG00000249659
2	lnc-EPS8L1-2	chr19:55671860-55672582	NONHSAT067998
3	lnc-EPS8L1-2	chr19:55671860-55672582	NONHSAT067999

Variant related genes	Relation type
ENSG00000267110	TF binding region
DNAAF3	TF binding region
TNNI3	TF binding region
ENSG00000105048	Chromatin interaction
ENSG00000160439	Chromatin interaction
ENSG00000239137	Chromatin interaction
ENSG00000125503	Chromatin interaction
ENSG00000108106	Chromatin interaction
ENSG00000129990	Chromatin interaction
ENSG00000167646	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11671293	0.84[TSI][hapmap]
rs3729709	1.00[JPT][hapmap]
rs3729841	0.88[GIH][hapmap]
rs3848617	1.00[ASW][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.99[MKK][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7249414	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7260320	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7260371	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs891187	0.91[MEX][hapmap];0.90[TSI][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	nsv534462	chr19:55028722-55683018	Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
2	nsv912451	chr19:55595687-55680746	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv912453	chr19:55672007-55690398	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:55669000-55672800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
2	chr19:55669200-55672800	Enhancers	Fetal Heart	heart
3	chr19:55669600-55673400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
4	chr19:55670800-55673800	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
5	chr19:55671000-55673000	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr19:55671400-55672600	Bivalent Enhancer	Fetal Muscle Leg	muscle
7	chr19:55671600-55672600	Bivalent Enhancer	Stomach Smooth Muscle	stomach
8	chr19:55671600-55672800	Bivalent Enhancer	Placenta	Placenta
9	chr19:55671600-55677600	Weak transcription	Right Atrium	heart
10	chr19:55671800-55672600	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr19:55671800-55677600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr19:55672000-55672600	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
13	chr19:55672000-55672600	Enhancers	Pancreas	Pancrea
14	chr19:55672000-55672800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
15	chr19:55672000-55672800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
16	chr19:55672000-55672800	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
17	chr19:55672000-55673000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
18	chr19:55672000-55673400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
19	chr19:55672000-55673400	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
20	chr19:55672000-55677200	Weak transcription	NHEK	skin
21	chr19:55672200-55672600	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr19:55672200-55672600	Flanking Active TSS	Right Ventricle	heart
23	chr19:55672200-55672600	Weak transcription	K562	blood
24	chr19:55672200-55673600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr19:55672200-55676800	Weak transcription	Hela-S3	cervix
26	chr19:55672400-55672600	Bivalent/Poised TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr19:55672400-55672600	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr19:55672400-55672600	Bivalent/Poised TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr19:55672400-55672600	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
30	chr19:55672400-55672600	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr19:55672400-55672600	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr19:55672400-55672600	Bivalent Enhancer	Brain Hippocampus Middle	brain
33	chr19:55672400-55672600	Enhancers	Left Ventricle	heart
34	chr19:55672400-55672600	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
35	chr19:55672400-55672600	ZNF genes & repeats	Spleen	Spleen
36	chr19:55672400-55672800	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
37	chr19:55672400-55672800	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
38	chr19:55672400-55672800	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
39	chr19:55672400-55672800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
40	chr19:55672400-55672800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
41	chr19:55672400-55672800	Flanking Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr19:55672400-55672800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr19:55672400-55673000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
44	chr19:55672400-55673000	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
45	chr19:55672400-55673000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr19:55672400-55673200	Active TSS	H9 Cell Line	embryonic stem cell
47	chr19:55672400-55673200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr19:55672400-55673400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
49	chr19:55672400-55673400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin

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