Variant report

Variant	rs2045754
Chromosome Location	chr19:53030848-53030849
allele	A/G
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	ELF1	chr19:53030076-53031232	GM12878	blood:	n/a	chr19:53030923-53030932 chr19:53030922-53030933 chr19:53030402-53030414 chr19:53030922-53030933 chr19:53030924-53030933
2	MAX	chr19:53030799-53031105	K562	blood:	n/a	chr19:53030956-53030965 chr19:53030855-53030865
3	GABPA	chr19:53030781-53031083	GM12878	blood:	n/a	chr19:53030856-53030865 chr19:53030903-53030912
4	RFX5	chr19:53030326-53031125	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr19:53030820-53031178	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr19:53030780-53031451	GM12878	blood:	n/a	n/a
7	POLR2A	chr19:53030218-53031233	SK-N-SH	brain:	n/a	n/a
8	GABPA	chr19:53030769-53031086	HepG2	liver:	n/a	chr19:53030856-53030865 chr19:53030903-53030912
9	GABPA	chr19:53030593-53031205	SK-N-SH	brain:	n/a	chr19:53030856-53030865 chr19:53030903-53030912
10	YY1	chr19:53030808-53031141	SK-N-SH_RA	brain:	n/a	n/a
11	POLR2A	chr19:53030794-53031666	K562	blood:	n/a	n/a
12	MXI1	chr19:53030279-53031517	HepG2	liver:	n/a	n/a
13	POLR2A	chr19:53030808-53031151	SK-N-SH	brain:	n/a	n/a
14	NR2F2	chr19:53030758-53031092	K562	blood:	n/a	n/a
15	SP1	chr19:53030240-53031117	K562	blood:	n/a	chr19:53030869-53030883 chr19:53030401-53030413 chr19:53030855-53030865 chr19:53030855-53030869 chr19:53030403-53030412 chr19:53030401-53030413 chr19:53030855-53030865 chr19:53030854-53030866 chr19:53030856-53030865 chr19:53030855-53030864 chr19:53030854-53030866
16	STAT1	chr19:53030501-53031360	GM12878	blood:	n/a	chr19:53031232-53031244
17	ELF1	chr19:53030148-53031258	SK-N-SH	brain:	n/a	chr19:53030923-53030932 chr19:53030922-53030933 chr19:53030402-53030414 chr19:53030922-53030933 chr19:53030924-53030933
18	SIN3AK20	chr19:53030821-53031158	H1-hESC	embryonic stem cell:	n/a	n/a
19	CREB1	chr19:53030240-53031223	GM12878	blood:	n/a	n/a
20	POLR2A	chr19:53030792-53031273	GM12891	blood:	n/a	n/a
21	POLR2A	chr19:53030219-53031162	PANC-1	pancreas:	n/a	n/a
22	POLR2A	chr19:53030653-53031294	GM12878	blood:	n/a	n/a
23	MAX	chr19:53030764-53031517	ECC-1	luminal epithelium:	n/a	chr19:53030956-53030965 chr19:53031414-53031424 chr19:53030855-53030865
24	MAZ	chr19:53030299-53031330	GM12878	blood:	n/a	chr19:53030956-53030965 chr19:53030855-53030865
25	POLR2A	chr19:53030366-53031287	HUVEC	blood vessel:	n/a	n/a
26	POLR2A	chr19:53030209-53031285	PBDE	blood:	n/a	n/a
27	POLR2A	chr19:53030287-53031193	GM18526	blood:	n/a	n/a
28	MAX	chr19:53030540-53031079	HepG2	liver:	n/a	chr19:53030956-53030965 chr19:53030855-53030865
29	CHD2	chr19:53030358-53031168	Hela-S3	cervix:	n/a	chr19:53030873-53030883 chr19:53030825-53030835
30	MYC	chr19:53030277-53031412	NB4	blood:	n/a	chr19:53030956-53030965 chr19:53030855-53030865
31	YY1	chr19:53030797-53031126	K562	blood:	n/a	n/a
32	POLR2A	chr19:53030821-53031167	HCT-116	colon:	n/a	n/a
33	TBP	chr19:53030325-53031277	K562	blood:	n/a	n/a
34	POLR2A	chr19:53030221-53031334	GM19099	blood:	n/a	n/a
35	TAF1	chr19:53030833-53031161	ECC-1	luminal epithelium:	n/a	n/a
36	SP1	chr19:53030350-53031088	HepG2	liver:	n/a	chr19:53030869-53030883 chr19:53030401-53030413 chr19:53030855-53030865 chr19:53030855-53030869 chr19:53030403-53030412 chr19:53030401-53030413 chr19:53030855-53030865 chr19:53030854-53030866 chr19:53030856-53030865 chr19:53030855-53030864 chr19:53030854-53030866
37	MXI1	chr19:53030477-53031148	Hela-S3	cervix:	n/a	n/a
38	RCOR1	chr19:53030282-53031088	K562	blood:	n/a	n/a
39	JUN	chr19:53030200-53031857	K562	blood:	n/a	n/a
40	POLR2A	chr19:53030362-53031210	NB4	blood:	n/a	n/a
41	MYC	chr19:53030304-53031311	MCF10A-Er-Src	breast:	n/a	chr19:53030956-53030965 chr19:53030855-53030865
42	MAX	chr19:53030379-53031308	Hela-S3	cervix:	n/a	chr19:53030956-53030965 chr19:53030855-53030865
43	POLR2A	chr19:53030193-53031190	GM18951	blood:	n/a	n/a
44	MAX	chr19:53030229-53031127	SK-N-SH	brain:	n/a	chr19:53030956-53030965 chr19:53030855-53030865
45	TAF1	chr19:53030839-53031121	GM12878	blood:	n/a	n/a
46	YY1	chr19:53030815-53031159	SK-N-SH_RA	brain:	n/a	n/a
47	ETS1	chr19:53030820-53031058	K562	blood:	n/a	chr19:53030924-53030941 chr19:53030924-53030935 chr19:53031027-53031040 chr19:53030925-53030935
48	RUNX3	chr19:53030815-53031055	GM12878	blood:	n/a	n/a
49	POLR2A	chr19:53030780-53031196	GM12892	blood:	n/a	n/a
50	SIN3A	chr19:53030306-53031292	GM12878	blood:	n/a	chr19:53030831-53030842

No.	Distal block	Cell Line	Cell type
1	chr19:53029127..53032188-chr19:53072538..53075129,3	K562	blood:
2	chr19:53029450..53032188-chr19:53072538..53074123,2	K562	blood:
3	chr19:53029459..53032258-chr19:53036873..53039549,6	MCF-7	breast:

Variant related genes	Relation type
ZNF808	TF binding region
ENSG00000167562	Chromatin interaction
ENSG00000198482	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11668903	0.81[AMR][1000 genomes]
rs2608522	0.89[ASN][1000 genomes]
rs2615586	0.81[ASN][1000 genomes]
rs2615587	0.81[ASN][1000 genomes]
rs2615588	0.83[ASN][1000 genomes]
rs2633513	0.81[ASN][1000 genomes]
rs2633514	0.81[ASN][1000 genomes]
rs2633517	0.90[ASN][1000 genomes]
rs2925976	0.81[ASN][1000 genomes]
rs368922	0.81[ASN][1000 genomes]
rs376595	0.89[ASN][1000 genomes]
rs396663	0.88[ASN][1000 genomes]
rs400709	0.88[ASN][1000 genomes]
rs410046	0.89[ASN][1000 genomes]
rs413751	0.89[ASN][1000 genomes]
rs413814	0.81[ASN][1000 genomes]
rs417599	0.89[ASN][1000 genomes]
rs422195	0.88[ASN][1000 genomes]
rs429367	0.90[ASN][1000 genomes]
rs434709	0.88[ASN][1000 genomes]
rs439618	0.88[ASN][1000 genomes]
rs440545	0.90[ASN][1000 genomes]
rs441850	0.82[ASN][1000 genomes]
rs445500	0.89[ASN][1000 genomes]
rs449671	0.81[ASN][1000 genomes]
rs4802971	0.89[ASN][1000 genomes]
rs4802972	0.89[ASN][1000 genomes]
rs529698	0.81[ASN][1000 genomes]
rs532449	0.81[ASN][1000 genomes]
rs62117197	0.85[ASN][1000 genomes]
rs62117198	0.86[ASN][1000 genomes]
rs62117199	0.87[ASN][1000 genomes]
rs62119356	0.81[AMR][1000 genomes]
rs62119359	0.88[ASN][1000 genomes]
rs656541	0.82[ASN][1000 genomes]
rs668882	0.81[ASN][1000 genomes]
rs685200	0.81[ASN][1000 genomes]
rs688646	0.89[ASN][1000 genomes]
rs781129	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1066537	chr19:52794424-53044977	Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv544060	chr19:52794424-53044977	ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv580026	chr19:52937100-53059872	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1063648	chr19:52938131-53041119	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1057296	chr19:52950339-53396986	Weak transcription Active TSS ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
6	nsv978841	chr19:52983057-53088237	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	esv3404701	chr19:52986895-53035152	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	esv3440535	chr19:52993529-53035203	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv1066717	chr19:52993620-53041995	Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv1064342	chr19:52996710-53041119	ZNF genes & repeats Active TSS Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv1055825	chr19:53001299-53037378	Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv1055859	chr19:53001299-53041119	Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
13	nsv1060656	chr19:53001299-53041995	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:53029400-53031200	Active TSS	Primary T cells from cord blood	blood
2	chr19:53029600-53031400	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr19:53029600-53032000	Active TSS	HUES48 Cell Line	embryonic stem cell
4	chr19:53029600-53032000	Active TSS	HSMM	muscle
5	chr19:53029600-53032200	Active TSS	Colonic Mucosa	Colon
6	chr19:53030000-53031000	Active TSS	HepG2	liver
7	chr19:53030000-53031200	Active TSS	Primary hematopoietic stem cells	blood
8	chr19:53030000-53031200	Active TSS	Brain Germinal Matrix	brain
9	chr19:53030000-53031400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr19:53030000-53031400	Active TSS	Breast Myoepithelial Primary Cells	Breast
11	chr19:53030000-53031400	Active TSS	Brain Hippocampus Middle	brain
12	chr19:53030000-53031400	Active TSS	Pancreas	Pancrea
13	chr19:53030000-53031400	Active TSS	Psoas Muscle	Psoas
14	chr19:53030000-53031400	Active TSS	Rectal Mucosa Donor 29	rectum
15	chr19:53030000-53031400	Active TSS	Rectal Smooth Muscle	rectum
16	chr19:53030000-53031400	Active TSS	Right Ventricle	heart
17	chr19:53030000-53031400	Active TSS	Stomach Smooth Muscle	stomach
18	chr19:53030000-53031400	Active TSS	Thymus	Thymus
19	chr19:53030000-53031600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr19:53030000-53031600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
21	chr19:53030000-53031600	Active TSS	Brain Anterior Caudate	brain
22	chr19:53030000-53031600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
23	chr19:53030000-53031600	Active TSS	Colon Smooth Muscle	Colon
24	chr19:53030000-53031600	Active TSS	Duodenum Smooth Muscle	Duodenum
25	chr19:53030000-53031600	Active TSS	NHLF	lung
26	chr19:53030000-53031600	Active TSS	Osteobl	bone
27	chr19:53030000-53031800	Active TSS	H1 Cell Line	embryonic stem cell
28	chr19:53030000-53031800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr19:53030000-53031800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr19:53030000-53031800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr19:53030000-53031800	Active TSS	Fetal Kidney	kidney
32	chr19:53030000-53031800	Active TSS	Right Atrium	heart
33	chr19:53030000-53032000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr19:53030000-53032000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr19:53030000-53032000	Active TSS	Fetal Intestine Small	intestine
36	chr19:53030000-53032000	Active TSS	HMEC	breast
37	chr19:53030000-53032200	Active TSS	HUES64 Cell Line	embryonic stem cell
38	chr19:53030000-53032400	Active TSS	iPS-15b Cell Line	embryonic stem cell
39	chr19:53030000-53032400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr19:53030000-53032600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr19:53030200-53031000	Active TSS	Primary T regulatory cells fromperipheralblood	blood
42	chr19:53030200-53031200	Active TSS	Placenta Amnion	Placenta Amnion
43	chr19:53030200-53031400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr19:53030200-53031400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
45	chr19:53030200-53031400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr19:53030200-53031400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr19:53030200-53031400	Active TSS	Brain Cingulate Gyrus	brain
48	chr19:53030200-53031400	Active TSS	Fetal Muscle Leg	muscle
49	chr19:53030200-53031400	Active TSS	Sigmoid Colon	Sigmoid Colon
50	chr19:53030200-53031400	Active TSS	Stomach Mucosa	stomach

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