Variant report

Variant	rs3826757
Chromosome Location	chr19:56153118-56153119
allele	C/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	MAX	chr19:56151221-56155795	A549	lung:	n/a	chr19:56155426-56155435 chr19:56151539-56151548 chr19:56151539-56151549 chr19:56151539-56151549 chr19:56155425-56155436 chr19:56151538-56151549
2	POLR2A	chr19:56151273-56155759	ECC-1	luminal epithelium:	n/a	n/a
3	POLR2A	chr19:56150319-56156666	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr19:56150228-56156269	GM12891	blood:	n/a	n/a
5	POLR2A	chr19:56150192-56156534	GM12878	blood:	n/a	n/a
6	POLR2A	chr19:56152771-56153363	Hela-S3	cervix:	n/a	n/a
7	YY1	chr19:56152911-56153269	GM12892	blood:	n/a	chr19:56153110-56153119 chr19:56153142-56153150
8	POLR2A	chr19:56151425-56153170	MCF-7	breast:	n/a	n/a
9	RCOR1	chr19:56152785-56153326	GM12878	blood:	n/a	n/a
10	YY1	chr19:56152999-56153281	GM12891	blood:	n/a	chr19:56153110-56153119 chr19:56153142-56153150
11	CHD2	chr19:56151532-56155316	Hela-S3	cervix:	n/a	chr19:56154963-56154973 chr19:56152366-56152373
12	BHLHE40	chr19:56152929-56153221	GM12878	blood:	n/a	n/a
13	POLR2A	chr19:56151715-56153148	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr19:56149778-56157300	PANC-1	pancreas:	n/a	n/a
15	BCL3	chr19:56152067-56153271	GM12878	blood:	n/a	chr19:56152354-56152363 chr19:56152485-56152494
16	MAZ	chr19:56151386-56153256	K562	blood:	n/a	chr19:56151539-56151548 chr19:56151539-56151549 chr19:56151539-56151549 chr19:56151538-56151549
17	BCL3	chr19:56151732-56155150	A549	lung:	n/a	chr19:56153847-56153856 chr19:56152354-56152363 chr19:56152485-56152494
18	POLR2A	chr19:56150010-56156634	MCF10A-Er-Src	breast:	n/a	n/a
19	POLR2A	chr19:56151299-56155891	MCF-7	breast:	n/a	n/a
20	POLR2A	chr19:56151990-56153336	A549	lung:	n/a	n/a
21	REST	chr19:56151929-56153150	H1-neurons	neurons:	n/a	chr19:56152785-56152795 chr19:56152735-56152748
22	POLR2A	chr19:56151264-56153383	K562	blood:	n/a	n/a
23	POLR2A	chr19:56151325-56156943	GM19099	blood:	n/a	n/a
24	POLR2A	chr19:56150270-56155844	PANC-1	pancreas:	n/a	n/a
25	POLR2A	chr19:56151962-56153304	HL-60	blood:	n/a	n/a
26	POLR2A	chr19:56151135-56153336	K562	blood:	n/a	n/a
27	POLR2A	chr19:56151350-56155716	GM18526	blood:	n/a	n/a
28	POLR2A	chr19:56151852-56153389	SK-N-MC	brain:	n/a	n/a
29	SPI1	chr19:56153105-56153354	GM12878	blood:	n/a	chr19:56153293-56153300 chr19:56153290-56153303
30	POLR2A	chr19:56151378-56156635	GM18951	blood:	n/a	n/a
31	MAX	chr19:56151283-56153174	HepG2	liver:	n/a	chr19:56151539-56151548 chr19:56151539-56151549 chr19:56151539-56151549 chr19:56151538-56151549
32	STAT5A	chr19:56151161-56153862	GM12878	blood:	n/a	chr19:56151811-56151818 chr19:56152748-56152760 chr19:56152799-56152807 chr19:56152675-56152687 chr19:56151740-56151752
33	POLR2A	chr19:56151205-56153389	GM12892	blood:	n/a	n/a
34	POLR2A	chr19:56151603-56155613	U87	brain:	n/a	n/a
35	SRF	chr19:56152889-56153205	GM12878	blood:	n/a	chr19:56153043-56153061 chr19:56153042-56153060 chr19:56153046-56153057 chr19:56153045-56153058 chr19:56153046-56153063 chr19:56153042-56153056 chr19:56153047-56153056 chr19:56153045-56153056 chr19:56153044-56153059 chr19:56153047-56153058 chr19:56153040-56153057
36	POLR2A	chr19:56151310-56156615	Raji	blood:	n/a	n/a
37	POLR2A	chr19:56146066-56155822	MCF10A-Er-Src	breast:	n/a	n/a
38	TCF12	chr19:56151963-56153219	A549	lung:	n/a	n/a
39	POLR2A	chr19:56151262-56156558	GM12878	blood:	n/a	n/a
40	POLR2A	chr19:56150509-56155890	PBDE	blood:	n/a	n/a
41	POLR2A	chr19:56151208-56155527	HCT-116	colon:	n/a	n/a
42	NFATC1	chr19:56151209-56153321	GM12878	blood:	n/a	n/a
43	POLR2A	chr19:56151377-56153674	HCT-116	colon:	n/a	n/a
44	CHD2	chr19:56152042-56153207	GM12878	blood:	n/a	chr19:56152366-56152373
45	POLR2A	chr19:56150387-56157088	GM18505	blood:	n/a	n/a
46	CTCF	chr19:56150241-56153137	SK-N-SH	brain:	n/a	chr19:56152319-56152332 chr19:56152316-56152329
47	POLR2A	chr19:56151277-56156546	GM15510	blood:	n/a	n/a
48	POLR2A	chr19:56153038-56153387	K562	blood:	n/a	n/a
49	BCL3	chr19:56151269-56155527	A549	lung:	n/a	chr19:56153847-56153856 chr19:56152354-56152363 chr19:56152485-56152494 chr19:56155304-56155317
50	SRF	chr19:56152965-56153140	GM12878	blood:	n/a	chr19:56153043-56153061 chr19:56153042-56153060 chr19:56153046-56153057 chr19:56153045-56153058 chr19:56153046-56153063 chr19:56153042-56153056 chr19:56153047-56153056 chr19:56153045-56153056 chr19:56153044-56153059 chr19:56153047-56153058 chr19:56153040-56153057

No.	Distal block	Cell Line	Cell type
1	chr19:55994990..55999125-chr19:56150596..56153745,4	K562	blood:
2	chr19:55813454..55816310-chr19:56151502..56153482,2	MCF-7	breast:
3	chr19:56113112..56115949-chr19:56151962..56154337,3	K562	blood:
4	chr19:56107792..56111497-chr19:56151607..56154571,3	MCF-7	breast:
5	chr19:55894292..55897074-chr19:56152142..56154833,2	MCF-7	breast:
6	chr19:56132811..56137423-chr19:56151241..56156557,5	MCF-7	breast:
7	chr19:55964915..55966958-chr19:56152410..56155336,2	K562	blood:
8	chr19:55628447..55630304-chr19:56152037..56154900,2	K562	blood:
9	chr19:56110523..56113100-chr19:56152133..56154992,3	K562	blood:
10	chr19:56134500..56138557-chr19:56151822..56155582,4	K562	blood:
11	chr19:55626366..55629144-chr19:56151698..56154505,2	MCF-7	breast:
12	chr19:56133203..56138391-chr19:56150309..56156340,8	K562	blood:
13	chr19:56109287..56112853-chr19:56149861..56154883,7	MCF-7	breast:
14	chr19:55627842..55630893-chr19:56150877..56153462,3	MCF-7	breast:
15	chr19:55996765..55998431-chr19:56152633..56154883,2	MCF-7	breast:
16	chr19:54973325..54975898-chr19:56151644..56153909,2	MCF-7	breast:
17	chr19:56152176..56154153-chr19:56826714..56828246,2	MCF-7	breast:
18	chr19:56115086..56118069-chr19:56150430..56156112,7	MCF-7	breast:
19	chr19:55917594..55920802-chr19:56150613..56153734,3	K562	blood:
20	chr19:56114376..56117189-chr19:56151962..56154337,3	K562	blood:
21	chr19:56152964..56155802-chr19:56186387..56188533,2	MCF-7	breast:
22	chr19:56152467..56154229-chr19:56171336..56173701,2	MCF-7	breast:

Variant related genes	Relation type
ZNF580	TF binding region
ZNF581	TF binding region
ENSG00000200646	Chromatin interaction
ENSG00000233493	Chromatin interaction
ENSG00000179943	Chromatin interaction
ENSG00000160469	Chromatin interaction
ENSG00000182909	Chromatin interaction
ENSG00000261221	Chromatin interaction
ENSG00000179922	Chromatin interaction
ENSG00000090971	Chromatin interaction
ENSG00000171443	Chromatin interaction
ENSG00000108107	Chromatin interaction
ENSG00000063241	Chromatin interaction
ENSG00000063244	Chromatin interaction
ENSG00000125503	Chromatin interaction
ENSG00000108106	Chromatin interaction
ENSG00000267549	Chromatin interaction
ENSG00000063245	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10403866	0.81[EUR][1000 genomes]
rs10410886	0.81[EUR][1000 genomes]
rs11084405	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2280255	0.85[ASN][1000 genomes]
rs2287791	0.83[ASN][1000 genomes]
rs28375493	0.85[ASN][1000 genomes]
rs310472	0.85[ASN][1000 genomes]
rs310473	0.82[ASN][1000 genomes]
rs3745446	0.87[ASN][1000 genomes]
rs4801526	0.85[ASN][1000 genomes]
rs523509	0.82[ASN][1000 genomes]
rs575274	0.88[ASN][1000 genomes]
rs610811	0.86[ASN][1000 genomes]
rs73613281	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912487	chr19:55977909-56215184	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
2	nsv912494	chr19:56026072-56215184	Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
3	nsv912498	chr19:56041848-56215184	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
4	nsv828643	chr19:56059280-56154823	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
5	nsv912500	chr19:56078722-56175515	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	86 gene(s)	inside rSNPs	diseases
6	nsv912501	chr19:56093365-56215184	Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
7	nsv428026	chr19:56130849-56423514	Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	82 gene(s)	inside rSNPs	diseases
8	nsv912503	chr19:56149077-56162776	Genic enhancers Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	30 gene(s)	inside rSNPs	diseases
9	nsv912504	chr19:56149077-56170415	Flanking Active TSS Genic enhancers Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	57 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	chr19:56151400-56153800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr19:56151400-56154000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr19:56151400-56154400	Active TSS	iPS-15b Cell Line	embryonic stem cell
4	chr19:56151600-56154200	Active TSS	HUES6 Cell Line	embryonic stem cell
5	chr19:56151600-56154400	Active TSS	HUES48 Cell Line	embryonic stem cell
6	chr19:56151600-56154800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
7	chr19:56151600-56155600	Active TSS	Ovary	ovary
8	chr19:56151600-56155800	Active TSS	Fetal Kidney	kidney
9	chr19:56151600-56156000	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr19:56151600-56156200	Active TSS	HUES64 Cell Line	embryonic stem cell
11	chr19:56151600-56156200	Active TSS	iPS-20b Cell Line	embryonic stem cell
12	chr19:56151800-56154200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr19:56151800-56154200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr19:56151800-56154200	Active TSS	Esophagus	oesophagus
15	chr19:56151800-56154400	Active TSS	iPS-18 Cell Line	embryonic stem cell
16	chr19:56151800-56154400	Active TSS	Colon Smooth Muscle	Colon
17	chr19:56151800-56154800	Flanking Active TSS	Primary B cells from cord blood	blood
18	chr19:56151800-56155000	Flanking Active TSS	Primary hematopoietic stem cells	blood
19	chr19:56151800-56155000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr19:56151800-56155000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr19:56151800-56155800	Active TSS	H9 Cell Line	embryonic stem cell
22	chr19:56151800-56156000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr19:56151800-56156000	Active TSS	Pancreatic Islets	Pancreatic Islet
24	chr19:56152000-56153200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
25	chr19:56152000-56153200	Active TSS	Gastric	stomach
26	chr19:56152000-56153400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr19:56152000-56153400	Active TSS	Fetal Heart	heart
28	chr19:56152000-56153400	Active TSS	Fetal Stomach	stomach
29	chr19:56152000-56153600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr19:56152000-56153600	Active TSS	NH-A	brain
31	chr19:56152000-56153800	Active TSS	Placenta Amnion	Placenta Amnion
32	chr19:56152000-56153800	Active TSS	Right Ventricle	heart
33	chr19:56152000-56153800	Active TSS	A549	lung
34	chr19:56152000-56153800	Active TSS	Osteobl	bone
35	chr19:56152000-56154000	Active TSS	Left Ventricle	heart
36	chr19:56152000-56154000	Active TSS	Psoas Muscle	Psoas
37	chr19:56152000-56154200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr19:56152000-56154200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr19:56152000-56154200	Active TSS	Aorta	Aorta
40	chr19:56152000-56154200	Active TSS	Duodenum Smooth Muscle	Duodenum
41	chr19:56152000-56154200	Active TSS	HepG2	liver
42	chr19:56152000-56154200	Active TSS	HSMMtube	muscle
43	chr19:56152000-56154400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr19:56152000-56154400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr19:56152000-56155800	Active TSS	H1 Cell Line	embryonic stem cell
46	chr19:56152200-56153200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr19:56152200-56153400	Active TSS	Primary T cells from cord blood	blood
48	chr19:56152200-56153400	Active TSS	Brain Inferior Temporal Lobe	brain
49	chr19:56152200-56153400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
50	chr19:56152200-56153400	Active TSS	Fetal Intestine Small	intestine

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