Variant report

Variant	rs566530903
Chromosome Location	chr19:56111971-56111972
allele	A/C
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	POLR2A	chr19:56111745-56112155	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr19:56111857-56112286	HepG2	liver:	n/a	n/a
3	YY1	chr19:56110210-56112179	SK-N-SH_RA	brain:	n/a	chr19:56111931-56111945 chr19:56110867-56110881 chr19:56111936-56111945 chr19:56110866-56110880 chr19:56111041-56111049 chr19:56111363-56111373 chr19:56111792-56111803 chr19:56111036-56111055 chr19:56111337-56111359 chr19:56111038-56111060 chr19:56111934-56111948 chr19:56111799-56111810 chr19:56110725-56110739 chr19:56111930-56111944 chr19:56111786-56111800
4	POLR2A	chr19:56110343-56112269	HCT-116	colon:	n/a	n/a
5	STAT5A	chr19:56111945-56112455	GM12878	blood:	n/a	chr19:56112189-56112201 chr19:56112244-56112256 chr19:56112048-56112060
6	TBP	chr19:56111894-56112123	H1-hESC	embryonic stem cell:	n/a	n/a
7	HCFC1	chr19:56109967-56112882	Hela-S3	cervix:	n/a	n/a
8	CREB1	chr19:56110197-56112202	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr19:56110403-56112396	HCT-116	colon:	n/a	n/a
10	MXI1	chr19:56110279-56112325	HepG2	liver:	n/a	n/a
11	CREB1	chr19:56110230-56112225	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr19:56111820-56112346	GM12892	blood:	n/a	n/a
13	TAF1	chr19:56110393-56112223	ECC-1	luminal epithelium:	n/a	n/a
14	HA-E2F1	chr19:56110713-56112124	Hela-S3	cervix:	n/a	chr19:56111952-56111962 chr19:56111568-56111575 chr19:56111586-56111597 chr19:56111508-56111518 chr19:56111568-56111575 chr19:56111931-56111941 chr19:56111371-56111378 chr19:56111506-56111515 chr19:56111371-56111378 chr19:56111568-56111575 chr19:56110870-56110880 chr19:56110725-56110735 chr19:56111586-56111598 chr19:56111371-56111378 chr19:56111936-56111945
15	POLR2A	chr19:56111908-56112889	MCF10A-Er-Src	breast:	n/a	n/a
16	POLR2A	chr19:56111917-56112327	GM12891	blood:	n/a	n/a
17	BHLHE40	chr19:56110278-56112129	GM12878	blood:	n/a	chr19:56111932-56111948
18	TCF12	chr19:56111696-56112044	GM12878	blood:	n/a	n/a
19	MAX	chr19:56110285-56112008	Hela-S3	cervix:	n/a	chr19:56111783-56111793 chr19:56110495-56110505
20	POLR2A	chr19:56110299-56112347	HUVEC	blood vessel:	n/a	n/a
21	MYC	chr19:56110264-56112022	K562	blood:	n/a	chr19:56111783-56111793 chr19:56110495-56110505
22	POLR2A	chr19:56110211-56112145	K562	blood:	n/a	n/a
23	POLR2A	chr19:56110141-56113242	HepG2	liver:	n/a	n/a
24	YY1	chr19:56110217-56112133	K562	blood:	n/a	chr19:56111931-56111945 chr19:56110867-56110881 chr19:56111936-56111945 chr19:56110866-56110880 chr19:56111041-56111049 chr19:56111363-56111373 chr19:56111792-56111803 chr19:56111036-56111055 chr19:56111337-56111359 chr19:56111038-56111060 chr19:56111934-56111948 chr19:56111799-56111810 chr19:56110725-56110739 chr19:56111930-56111944 chr19:56111786-56111800
25	MTA3	chr19:56111851-56112846	GM12878	blood:	n/a	n/a
26	POLR2A	chr19:56110379-56112340	MCF-7	breast:	n/a	n/a
27	EGR1	chr19:56110675-56112148	ECC-1	luminal epithelium:	n/a	chr19:56111967-56111989 chr19:56111692-56111705 chr19:56111935-56111945 chr19:56111724-56111734 chr19:56110797-56110807 chr19:56111824-56111834 chr19:56111506-56111515 chr19:56110870-56110880 chr19:56111689-56111703 chr19:56111905-56111914 chr19:56111972-56111985 chr19:56111973-56111982 chr19:56110920-56110934 chr19:56110867-56110880 chr19:56111972-56111982 chr19:56111733-56111742 chr19:56111931-56111944 chr19:56111907-56111916
28	NRF1	chr19:56110703-56112031	GM12878	blood:	n/a	chr19:56111579-56111588 chr19:56111729-56111738 chr19:56111732-56111746 chr19:56111729-56111743 chr19:56111504-56111515 chr19:56111505-56111519 chr19:56111939-56111948 chr19:56111505-56111516 chr19:56111502-56111516 chr19:56111505-56111514 chr19:56111906-56111920 chr19:56111731-56111740
29	MYC	chr19:56111959-56111992	MCF-7	breast:	n/a	n/a
30	TCF3	chr19:56111309-56112084	GM12878	blood:	n/a	chr19:56111859-56111868 chr19:56111856-56111871
31	JUN	chr19:56110074-56112209	K562	blood:	n/a	chr19:56111585-56111594 chr19:56110711-56110720 chr19:56111987-56111996 chr19:56111961-56111970
32	POLR2A	chr19:56110193-56112299	HUVEC	blood vessel:	n/a	n/a
33	YY1	chr19:56110202-56112412	SK-N-SH	brain:	n/a	chr19:56111931-56111945 chr19:56110867-56110881 chr19:56111936-56111945 chr19:56110866-56110880 chr19:56111041-56111049 chr19:56111363-56111373 chr19:56111792-56111803 chr19:56111036-56111055 chr19:56111337-56111359 chr19:56111038-56111060 chr19:56111934-56111948 chr19:56111799-56111810 chr19:56110725-56110739 chr19:56112299-56112318 chr19:56111930-56111944 chr19:56111786-56111800
34	POLR2A	chr19:56111962-56112304	HepG2	liver:	n/a	n/a
35	POLR2A	chr19:56110205-56112252	HL-60	blood:	n/a	n/a
36	MAX	chr19:56110274-56112336	HepG2	liver:	n/a	chr19:56111783-56111793 chr19:56110495-56110505
37	YY1	chr19:56111807-56112233	GM12878	blood:	n/a	chr19:56111931-56111945 chr19:56111936-56111945 chr19:56111934-56111948 chr19:56111930-56111944
38	CREB1	chr19:56110208-56112369	HepG2	liver:	n/a	n/a
39	GABPA	chr19:56111829-56112057	HepG2	liver:	n/a	chr19:56111939-56111948 chr19:56111906-56111920
40	TAF1	chr19:56111784-56112306	H1-neurons	neurons:	n/a	n/a
41	TAF1	chr19:56111807-56112175	H1-hESC	embryonic stem cell:	n/a	n/a
42	THAP1	chr19:56111821-56112081	K562	blood:	n/a	n/a
43	ELF1	chr19:56111347-56112162	K562	blood:	n/a	chr19:56111793-56111805 chr19:56111580-56111592
44	RUNX3	chr19:56111922-56112391	GM12878	blood:	n/a	n/a
45	POLR2A	chr19:56110456-56112419	MCF-7	breast:	n/a	n/a
46	GABPA	chr19:56111837-56112039	HepG2	liver:	n/a	chr19:56111939-56111948 chr19:56111906-56111920
47	CHD2	chr19:56110449-56112122	H1-hESC	embryonic stem cell:	n/a	chr19:56112040-56112050
48	PML	chr19:56110218-56112285	GM12878	blood:	n/a	n/a
49	CEBPD	chr19:56111317-56112188	HepG2	liver:	n/a	n/a
50	E2F6	chr19:56111262-56112107	K562	blood:	n/a	chr19:56111370-56111378 chr19:56111952-56111962 chr19:56111568-56111575 chr19:56111508-56111518 chr19:56111568-56111575 chr19:56111931-56111941 chr19:56111371-56111378 chr19:56111506-56111515 chr19:56111371-56111378 chr19:56111568-56111575 chr19:56111586-56111598 chr19:56111371-56111378 chr19:56111936-56111945

No.	Distal block	Cell Line	Cell type
1	chr19:55986000..55989537-chr19:56108522..56112833,7	MCF-7	breast:
2	chr19:55726839..55729396-chr19:56109968..56112582,3	K562	blood:
3	chr19:56054458..56057373-chr19:56110132..56112985,3	MCF-7	breast:
4	chr19:56110029..56112023-chr19:56153492..56156368,2	K562	blood:
5	chr19:56109729..56112451-chr19:56165377..56168122,5	MCF-7	breast:
6	chr19:55896562..55899346-chr19:56111616..56113771,2	MCF-7	breast:
7	chr19:56109995..56114029-chr19:56145200..56149074,4	MCF-7	breast:
8	chr19:55986046..55989016-chr19:56110567..56114260,3	K562	blood:
9	chr19:56111889..56113389-chr19:56150627..56153013,2	K562	blood:
10	chr19:56110653..56113509-chr19:56160158..56165183,5	MCF-7	breast:
11	chr19:55789004..55791837-chr19:56110524..56113034,2	K562	blood:
12	chr19:55986419..55989388-chr19:56109213..56112341,4	K562	blood:
13	chr1:28832112..28832968-chr19:56111203..56112184,2	Hela-S3	cervix:
14	chr19:56109380..56112832-chr19:56163189..56166704,4	K562	blood:
15	chr19:55685793..55687332-chr19:56110126..56112536,2	K562	blood:
16	chr19:56110415..56112373-chr19:56134518..56138349,4	MCF-7	breast:
17	chr19:56110428..56112493-chr19:56168408..56170811,2	MCF-7	breast:
18	chr19:55917650..55919623-chr19:56109574..56112521,4	MCF-7	breast:
19	chr19:56110522..56112658-chr19:56163189..56166668,4	K562	blood:
20	chr19:56109378..56114662-chr19:56134412..56139001,15	K562	blood:
21	chr19:55972027..55974548-chr19:56111000..56113265,2	MCF-7	breast:
22	chr19:56087311..56094258-chr19:56108819..56113699,11	K562	blood:
23	chr19:56087628..56093963-chr19:56108517..56113906,9	MCF-7	breast:
24	chr19:56109287..56112853-chr19:56149861..56154883,7	MCF-7	breast:
25	chr19:55685793..55687548-chr19:56110126..56112399,2	K562	blood:
26	chr19:55590451..55592160-chr19:56109992..56112858,2	K562	blood:
27	chr19:56110523..56113100-chr19:56152133..56154992,3	K562	blood:
28	chr19:56091409..56094452-chr19:56108819..56113428,6	K562	blood:
29	chr19:55917877..55920503-chr19:56111114..56113096,2	K562	blood:
30	chr19:56110285..56113089-chr19:56164482..56167654,4	MCF-7	breast:
31	chr19:55971482..55974428-chr19:56110628..56113037,3	K562	blood:
32	chr19:55996873..55998600-chr19:56111069..56112624,2	K562	blood:

Variant related genes	Relation type
ZNF524	TF binding region
FIZ1	TF binding region
ZNF865	TF binding region
ENSG00000108106	Chromatin interaction
ENSG00000180198	Chromatin interaction
ENSG00000108107	Chromatin interaction
ENSG00000063244	Chromatin interaction
ENSG00000197483	Chromatin interaction
ENSG00000218891	Chromatin interaction
ENSG00000171425	Chromatin interaction
ENSG00000242125	Chromatin interaction
ENSG00000133265	Chromatin interaction
ENSG00000179922	Chromatin interaction
ENSG00000269859	Chromatin interaction
ENSG00000267730	Chromatin interaction
ENSG00000231274	Chromatin interaction
ENSG00000090971	Chromatin interaction
ENSG00000213015	Chromatin interaction
ENSG00000129990	Chromatin interaction
ENSG00000131037	Chromatin interaction
ENSG00000173581	Chromatin interaction
ENSG00000063241	Chromatin interaction
ENSG00000267649	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912473	chr19:55874642-56145428	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
2	nsv912486	chr19:55977909-56145428	Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
3	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
4	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
5	nsv912495	chr19:56033088-56132661	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	nsv912496	chr19:56040051-56145428	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
7	nsv912497	chr19:56041848-56145428	Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
8	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
9	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
10	nsv912499	chr19:56071293-56132487	Flanking Active TSS Genic enhancers Active TSS Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
11	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
12	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
13	nsv912502	chr19:56099884-56138575	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
14	esv3376919	chr19:56110840-56112888	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	31 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	chr19:56109000-56112400	Active TSS	H9 Cell Line	embryonic stem cell
2	chr19:56109600-56112000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr19:56109800-56112000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr19:56109800-56112200	Active TSS	Duodenum Mucosa	Duodenum
5	chr19:56109800-56112200	Active TSS	Stomach Smooth Muscle	stomach
6	chr19:56109800-56112400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr19:56109800-56112400	Active TSS	Thymus	Thymus
8	chr19:56109800-56112400	Active TSS	NHDF-Ad	bronchial
9	chr19:56109800-56112600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr19:56109800-56113000	Active TSS	Brain Germinal Matrix	brain
11	chr19:56110000-56112200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr19:56110000-56112200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr19:56110000-56112200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr19:56110000-56112200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr19:56110000-56112200	Active TSS	Brain Cingulate Gyrus	brain
16	chr19:56110000-56112200	Active TSS	Brain Hippocampus Middle	brain
17	chr19:56110000-56112200	Active TSS	HMEC	breast
18	chr19:56110000-56112200	Active TSS	HSMM	muscle
19	chr19:56110000-56112200	Active TSS	HSMMtube	muscle
20	chr19:56110000-56112800	Active TSS	Psoas Muscle	Psoas
21	chr19:56110200-56112000	Active TSS	Primary T cells from cord blood	blood
22	chr19:56110200-56112000	Active TSS	Primary hematopoietic stem cells short term culture	blood
23	chr19:56110200-56112000	Active TSS	Primary T regulatory cells fromperipheralblood	blood
24	chr19:56110200-56112000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr19:56110200-56112000	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr19:56110200-56112000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr19:56110200-56112000	Active TSS	Fetal Muscle Trunk	muscle
28	chr19:56110200-56112200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr19:56110200-56112200	Active TSS	HUES48 Cell Line	embryonic stem cell
30	chr19:56110200-56112200	Active TSS	iPS-18 Cell Line	embryonic stem cell
31	chr19:56110200-56112200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr19:56110200-56112200	Active TSS	Primary neutrophils fromperipheralblood	blood
33	chr19:56110200-56112200	Active TSS	Muscle Satellite Cultured Cells	--
34	chr19:56110200-56112200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr19:56110200-56112200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr19:56110200-56112200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
37	chr19:56110200-56112200	Active TSS	Colon Smooth Muscle	Colon
38	chr19:56110200-56112200	Active TSS	Fetal Brain Female	brain
39	chr19:56110200-56112200	Active TSS	A549	lung
40	chr19:56110200-56112200	Active TSS	GM12878-XiMat	blood
41	chr19:56110200-56112200	Active TSS	HUVEC	blood vessel
42	chr19:56110200-56112200	Active TSS	Monocytes-CD14+_RO01746	blood
43	chr19:56110200-56112200	Active TSS	NH-A	brain
44	chr19:56110200-56112200	Active TSS	NHLF	lung
45	chr19:56110200-56112400	Active TSS	ES-I3 Cell Line	embryonic stem cell
46	chr19:56110200-56112400	Active TSS	H1 Cell Line	embryonic stem cell
47	chr19:56110200-56112400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr19:56110200-56112400	Active TSS	HUES6 Cell Line	embryonic stem cell
49	chr19:56110200-56112400	Active TSS	iPS-15b Cell Line	embryonic stem cell
50	chr19:56110200-56112400	Active TSS	iPS-20b Cell Line	embryonic stem cell

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