Variant report

Variant	rs2927459
Chromosome Location	chr19:45251505-45251506
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	MAZ	chr19:45250301-45252241	GM12878	blood:	n/a	chr19:45250878-45250887
2	CEBPB	chr19:45251273-45251544	H1-hESC	embryonic stem cell:	n/a	n/a
3	GATA2	chr19:45250994-45251636	HUVEC	blood vessel:	n/a	n/a
4	SMC3	chr19:45251340-45251513	HepG2	liver:	n/a	n/a
5	ELK1	chr19:45251367-45251555	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr19:45250600-45251742	SK-N-MC	brain:	n/a	n/a
7	MAX	chr19:45250518-45251593	SK-N-SH	brain:	n/a	chr19:45250878-45250887
8	ZBTB33	chr19:45250651-45251662	A549	lung:	n/a	n/a
9	RCOR1	chr19:45250786-45251707	GM12878	blood:	n/a	n/a
10	MAZ	chr19:45250381-45252178	Hela-S3	cervix:	n/a	chr19:45250878-45250887
11	SMC3	chr19:45250473-45251686	Hela-S3	cervix:	n/a	chr19:45250753-45250763 chr19:45250639-45250649
12	EP300	chr19:45251394-45252074	SK-N-SH_RA	brain:	n/a	chr19:45251827-45251843 chr19:45251823-45251839
13	POLR2A	chr19:45250618-45251632	HCT-116	colon:	n/a	n/a
14	POLR2A	chr19:45250230-45252136	PFSK-1	brain:	n/a	n/a
15	POLR2A	chr19:45251370-45252138	K562	blood:	n/a	n/a
16	MAX	chr19:45251472-45252071	GM12878	blood:	n/a	n/a
17	ZNF143	chr19:45250524-45251678	H1-hESC	embryonic stem cell:	n/a	n/a
18	EP300	chr19:45250387-45252152	SK-N-SH	brain:	n/a	chr19:45251827-45251843 chr19:45251823-45251839
19	ARID3A	chr19:45251363-45251524	K562	blood:	n/a	n/a
20	GATA3	chr19:45250389-45252188	A549	lung:	n/a	n/a
21	NRF1	chr19:45250731-45251600	GM12878	blood:	n/a	chr19:45250751-45250760
22	SP1	chr19:45249857-45252171	A549	lung:	n/a	chr19:45250751-45250760 chr19:45250749-45250760 chr19:45250674-45250684 chr19:45250750-45250760 chr19:45250750-45250764 chr19:45250749-45250761 chr19:45250793-45250802 chr19:45250674-45250683 chr19:45250850-45250864 chr19:45250750-45250759 chr19:45250673-45250685 chr19:45250674-45250683 chr19:45250674-45250688 chr19:45250750-45250759 chr19:45250817-45250828 chr19:45250674-45250684 chr19:45250675-45250684 chr19:45250801-45250812 chr19:45250673-45250685 chr19:45250749-45250761 chr19:45250750-45250760 chr19:45250115-45250125
23	JUND	chr19:45251350-45251693	K562	blood:	n/a	n/a
24	TAF1	chr19:45250764-45251678	PFSK-1	brain:	n/a	n/a
25	RCOR1	chr19:45249356-45252341	IMR90	lung:	n/a	n/a
26	POLR2A	chr19:45250479-45252237	K562	blood:	n/a	n/a
27	NFIC	chr19:45250494-45252125	SK-N-SH	brain:	n/a	n/a
28	EP300	chr19:45250659-45252182	GM12878	blood:	n/a	chr19:45251827-45251843 chr19:45251823-45251839
29	POLR2A	chr19:45251186-45251670	A549	lung:	n/a	n/a
30	POLR2A	chr19:45251130-45251680	HUVEC	blood vessel:	n/a	n/a
31	SPI1	chr19:45251207-45251508	GM12878	blood:	n/a	n/a
32	JUND	chr19:45250219-45252555	A549	lung:	n/a	chr19:45250880-45250887 chr19:45252543-45252552 chr19:45250877-45250888 chr19:45252545-45252554 chr19:45250716-45250724 chr19:45250875-45250886 chr19:45252546-45252555 chr19:45252542-45252551 chr19:45250879-45250887 chr19:45250845-45250854 chr19:45250879-45250887 chr19:45252544-45252553
33	TBL1XR1	chr19:45251498-45251711	K562	blood:	n/a	n/a
34	NR2F2	chr19:45251315-45252145	MCF-7	breast:	n/a	n/a
35	POLR2A	chr19:45250248-45251693	U87	brain:	n/a	n/a
36	ZBTB7A	chr19:45250531-45252587	ECC-1	luminal epithelium:	n/a	n/a
37	POLR2A	chr19:45250446-45252250	GM19193	blood:	n/a	n/a
38	TCF7L2	chr19:45251245-45252285	HCT-116	colon:	n/a	n/a
39	FOS	chr19:45251492-45251538	MCF10A-Er-Src	breast:	n/a	n/a
40	REST	chr19:45251172-45251676	A549	lung:	n/a	n/a
41	NR3C1	chr19:45250072-45251675	A549	lung:	n/a	chr19:45250716-45250725
42	NFIC	chr19:45250579-45251663	ECC-1	luminal epithelium:	n/a	n/a
43	FOSL2	chr19:45249383-45251814	A549	lung:	n/a	chr19:45250880-45250887 chr19:45250716-45250724 chr19:45250875-45250886 chr19:45250879-45250887 chr19:45250845-45250854 chr19:45250879-45250887
44	POLR2A	chr19:45250596-45252356	HUVEC	blood vessel:	n/a	n/a
45	EGR1	chr19:45251401-45251968	K562	blood:	n/a	n/a
46	POLR2A	chr19:45250493-45251684	HUVEC	blood vessel:	n/a	n/a
47	REST	chr19:45249690-45251673	A549	lung:	n/a	n/a
48	CEBPB	chr19:45251465-45251929	Hela-S3	cervix:	n/a	n/a
49	EP300	chr19:45250419-45252259	ECC-1	luminal epithelium:	n/a	chr19:45251827-45251843 chr19:45251823-45251839
50	PBX3	chr19:45249921-45252169	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:45164861..45166953-chr19:45250378..45253353,2	MCF-7	breast:
2	chr19:45173518..45176542-chr19:45249418..45252711,3	MCF-7	breast:
3	chr19:45250646..45253385-chr19:45348787..45352398,5	MCF-7	breast:
4	chr19:45180699..45183749-chr19:45249057..45252629,3	MCF-7	breast:
5	chr19:45249129..45253567-chr19:45309146..45313529,6	MCF-7	breast:
6	chr19:45250268..45252334-chr19:45593239..45597540,3	MCF-7	breast:
7	chr19:45250044..45254049-chr19:45347224..45351011,6	MCF-7	breast:
8	chr19:45250785..45254453-chr19:45309921..45313662,4	MCF-7	breast:
9	chr19:45222394..45233722-chr19:45248498..45258065,33	MCF-7	breast:

Variant related genes	Relation type
BCL3	TF binding region
ENSG00000252200	Chromatin interaction
ENSG00000267348	Chromatin interaction
ENSG00000104866	Chromatin interaction
ENSG00000130202	Chromatin interaction
ENSG00000187244	Chromatin interaction
ENSG00000186567	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10416418	0.86[ASN][1000 genomes]
rs1079086	0.86[AFR][1000 genomes]
rs11878508	0.86[ASN][1000 genomes]
rs11881529	0.86[ASN][1000 genomes]
rs2965170	0.84[AFR][1000 genomes]
rs56015301	0.86[ASN][1000 genomes]
rs56101375	0.86[ASN][1000 genomes]
rs57034040	0.86[ASN][1000 genomes]
rs58841331	0.86[ASN][1000 genomes]
rs59644378	0.86[ASN][1000 genomes]
rs73936950	0.86[ASN][1000 genomes]
rs73936951	0.86[ASN][1000 genomes]
rs73936952	0.86[ASN][1000 genomes]
rs73936953	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912116	chr19:45146103-45298069	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS 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 miRNA	29 gene(s)	inside rSNPs	diseases
2	nsv833841	chr19:45208486-45308043	Enhancers Bivalent/Poised TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
3	esv3335183	chr19:45225161-45253316	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	esv3324918	chr19:45250737-45253285	Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	esv3447789	chr19:45251012-45253160	Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 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	chr19:45243800-45252000	Weak transcription	Gastric	stomach
2	chr19:45248200-45251600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
3	chr19:45249800-45251600	Flanking Active TSS	Stomach Smooth Muscle	stomach
4	chr19:45249800-45253200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
5	chr19:45250000-45251600	Flanking Active TSS	Fetal Intestine Small	intestine
6	chr19:45250200-45251600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr19:45250200-45251600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr19:45250200-45251600	Flanking Active TSS	GM12878-XiMat	blood
9	chr19:45250200-45252400	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
10	chr19:45250200-45252800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
11	chr19:45250200-45252800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
12	chr19:45250200-45252800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
13	chr19:45250400-45251600	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
14	chr19:45250400-45251600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
15	chr19:45250400-45251600	Flanking Active TSS	Primary B cells from peripheral blood	blood
16	chr19:45250400-45251600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
17	chr19:45250400-45251600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
18	chr19:45250400-45251600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
19	chr19:45250400-45251600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
20	chr19:45250400-45251600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
21	chr19:45250400-45251600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr19:45250400-45251600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
23	chr19:45250400-45251600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
24	chr19:45250400-45251600	Flanking Active TSS	Fetal Muscle Trunk	muscle
25	chr19:45250400-45251600	Flanking Active TSS	Fetal Muscle Leg	muscle
26	chr19:45250400-45251600	Bivalent Enhancer	Dnd41	blood
27	chr19:45250400-45252600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
28	chr19:45250400-45252600	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr19:45250400-45252600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
30	chr19:45250400-45252800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr19:45250400-45252800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr19:45250400-45252800	Active TSS	Psoas Muscle	Psoas
33	chr19:45250400-45253200	Active TSS	Brain Inferior Temporal Lobe	brain
34	chr19:45250400-45254000	Active TSS	Sigmoid Colon	Sigmoid Colon
35	chr19:45250600-45251600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
36	chr19:45250600-45251600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr19:45250600-45251600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
38	chr19:45250600-45251600	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
39	chr19:45250600-45251600	Flanking Active TSS	Placenta	Placenta
40	chr19:45250600-45252400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
41	chr19:45250600-45252400	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr19:45250600-45252600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
43	chr19:45250600-45252600	Active TSS	Colon Smooth Muscle	Colon
44	chr19:45250600-45252600	Active TSS	Placenta Amnion	Placenta Amnion
45	chr19:45250600-45252600	Active TSS	Rectal Smooth Muscle	rectum
46	chr19:45250600-45252800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
47	chr19:45250600-45252800	Active TSS	Duodenum Mucosa	Duodenum
48	chr19:45250600-45253000	Active TSS	Right Ventricle	heart
49	chr19:45250600-45253000	Active TSS	HSMM	muscle
50	chr19:45250600-45253200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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