Variant report

Variant	rs11879688
Chromosome Location	chr19:56167756-56167757
allele	A/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	POLR2A	chr19:56164855-56168213	PANC-1	pancreas:	n/a	n/a
2	HCFC1	chr19:56164938-56168188	Hela-S3	cervix:	n/a	n/a
3	HEY1	chr19:56167387-56168350	K562	blood:	n/a	n/a
4	IRF1	chr19:56166316-56168146	K562	blood:	n/a	chr19:56166942-56166956
5	GATA2	chr19:56166506-56168052	SH-SY5Y	brain:	n/a	chr19:56166879-56166890 chr19:56167343-56167353 chr19:56167338-56167359 chr19:56167345-56167352 chr19:56167340-56167356 chr19:56167345-56167352 chr19:56167345-56167352 chr19:56167340-56167356
6	POLR2A	chr19:56164941-56169020	GM12878	blood:	n/a	n/a
7	CHD1	chr19:56166347-56167759	H1-hESC	embryonic stem cell:	n/a	n/a
8	WRNIP1	chr19:56166793-56170333	GM12878	blood:	n/a	n/a
9	POLR2A	chr19:56164851-56170437	PANC-1	pancreas:	n/a	n/a
10	IRF1	chr19:56164969-56168457	K562	blood:	n/a	chr19:56165607-56165620 chr19:56165602-56165619 chr19:56165700-56165720 chr19:56165608-56165618 chr19:56166942-56166956 chr19:56165608-56165622 chr19:56165604-56165618 chr19:56165606-56165626 chr19:56165607-56165618
11	MTA3	chr19:56166261-56167895	GM12878	blood:	n/a	n/a
12	POLR2A	chr19:56164914-56168119	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr19:56164619-56167840	HepG2	liver:	n/a	n/a
14	REST	chr19:56166301-56168198	A549	lung:	n/a	chr19:56166748-56166761 chr19:56166745-56166758 chr19:56167749-56167769
15	POLR2A	chr19:56164956-56169503	K562	blood:	n/a	n/a
16	POLR2A	chr19:56164901-56167760	K562	blood:	n/a	n/a
17	POLR2A	chr19:56166282-56168009	GM12892	blood:	n/a	n/a
18	GATA3	chr19:56167129-56167908	SH-SY5Y	brain:	n/a	chr19:56167343-56167353 chr19:56167338-56167359 chr19:56167345-56167352 chr19:56167340-56167356 chr19:56167345-56167352 chr19:56167345-56167352 chr19:56167340-56167356
19	MYC	chr19:56164961-56168359	K562	blood:	n/a	chr19:56166757-56166772 chr19:56167157-56167173 chr19:56166761-56166771 chr19:56166756-56166775 chr19:56166759-56166774 chr19:56166762-56166771 chr19:56166759-56166768 chr19:56166760-56166770 chr19:56166761-56166770
20	POLR2A	chr19:56166277-56169272	GM12878	blood:	n/a	n/a
21	POLR2A	chr19:56164953-56167781	K562	blood:	n/a	n/a
22	TBL1XR1	chr19:56167709-56168182	GM12878	blood:	n/a	n/a
23	POLR2A	chr19:56164926-56168745	GM12891	blood:	n/a	n/a
24	POLR2A	chr19:56166287-56167854	GM12892	blood:	n/a	n/a
25	POLR2A	chr19:56164853-56167831	GM12878	blood:	n/a	n/a
26	POLR2A	chr19:56164963-56167785	GM12878	blood:	n/a	n/a
27	JUN	chr19:56164949-56168739	K562	blood:	n/a	chr19:56165258-56165272 chr19:56166577-56166586
28	POLR2A	chr19:56164827-56168951	SK-N-MC	brain:	n/a	n/a
29	CHD1	chr19:56166327-56168561	IMR90	lung:	n/a	n/a
30	MXI1	chr19:56164856-56169392	SK-N-SH	brain:	n/a	chr19:56165279-56165294 chr19:56166760-56166769 chr19:56165281-56165296 chr19:56166762-56166771
31	BCL3	chr19:56166276-56167759	A549	lung:	n/a	chr19:56166539-56166548 chr19:56166911-56166920 chr19:56166917-56166926
32	POLR2A	chr19:56164951-56167821	HepG2	liver:	n/a	n/a
33	POLR2A	chr19:56164926-56167852	Hela-S3	cervix:	n/a	n/a
34	MAX	chr19:56164960-56167783	A549	lung:	n/a	chr19:56166757-56166772 chr19:56167157-56167173 chr19:56166761-56166771 chr19:56166756-56166775 chr19:56166759-56166774 chr19:56166762-56166771 chr19:56166759-56166768 chr19:56166760-56166770 chr19:56166761-56166770
35	SIN3A	chr19:56166375-56167980	H1-hESC	embryonic stem cell:	n/a	chr19:56166762-56166771 chr19:56166745-56166758
36	TBL1XR1	chr19:56167508-56168116	K562	blood:	n/a	n/a
37	POLR2A	chr19:56166254-56167824	HL-60	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:56135761..56137279-chr19:56166087..56167869,2	MCF-7	breast:
2	chr19:56164975..56168855-chr19:56176069..56182259,9	MCF-7	breast:
3	chr19:55986503..55989848-chr19:56164025..56167760,5	K562	blood:
4	chr19:56165204..56168088-chr19:56651419..56654921,3	MCF-7	breast:
5	chr19:56165463..56168899-chr19:56631045..56633379,3	K562	blood:
6	chr19:56109729..56112451-chr19:56165377..56168122,5	MCF-7	breast:
7	chr19:56164666..56171824-chr19:56183341..56192911,16	MCF-7	breast:
8	chr19:56165703..56169980-chr19:56194386..56196896,5	MCF-7	breast:
9	chr19:55627421..55629071-chr19:56166474..56168541,2	MCF-7	breast:
10	chr19:55850613..55852119-chr19:56166654..56168818,2	K562	blood:
11	chr19:56134733..56137004-chr19:56165358..56168098,3	MCF-7	breast:
12	chr19:56165194..56167874-chr19:56829304..56831856,2	K562	blood:
13	chr19:56134221..56137618-chr19:56162633..56168532,10	K562	blood:

Variant related genes	Relation type
U2AF2	TF binding region
ENSG00000197483	Chromatin interaction
ENSG00000179922	Chromatin interaction
ENSG00000267523	Chromatin interaction
ENSG00000125503	Chromatin interaction
ENSG00000267096	Chromatin interaction
ENSG00000179943	Chromatin interaction
ENSG00000133247	Chromatin interaction
ENSG00000269859	Chromatin interaction
ENSG00000142409	Chromatin interaction
ENSG00000213014	Chromatin interaction
ENSG00000167685	Chromatin interaction
ENSG00000171443	Chromatin interaction
ENSG00000267531	Chromatin interaction
ENSG00000063245	Chromatin interaction
ENSG00000211571	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs10415985	1.00[AMR][1000 genomes]
rs11879279	1.00[AMR][1000 genomes]
rs8106573	1.00[AMR][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	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
5	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
6	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
7	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
8	nsv833882	chr19:56158633-56326564	Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
9	nsv1061024	chr19:56167101-56217359	Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 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	chr19:56163400-56167800	Active TSS	iPS-15b Cell Line	embryonic stem cell
2	chr19:56163400-56168000	Active TSS	H9 Cell Line	embryonic stem cell
3	chr19:56163400-56168200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr19:56163600-56167800	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr19:56163600-56167800	Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr19:56163600-56168000	Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr19:56164200-56168000	Active TSS	H1 Cell Line	embryonic stem cell
8	chr19:56164400-56167800	Active TSS	iPS-18 Cell Line	embryonic stem cell
9	chr19:56164400-56168000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr19:56164400-56168000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr19:56164400-56168400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr19:56164600-56167800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr19:56164600-56167800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr19:56164800-56167800	Active TSS	Fetal Lung	lung
15	chr19:56164800-56167800	Active TSS	HMEC	breast
16	chr19:56164800-56168000	Active TSS	HUES48 Cell Line	embryonic stem cell
17	chr19:56164800-56168000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
18	chr19:56164800-56168200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr19:56164800-56168200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr19:56165000-56167800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr19:56165000-56167800	Active TSS	Muscle Satellite Cultured Cells	--
22	chr19:56165000-56168000	Active TSS	HSMMtube	muscle
23	chr19:56165000-56168200	Active TSS	Fetal Intestine Small	intestine
24	chr19:56165200-56167800	Active TSS	Primary T helper cells PMA-I stimulated	--
25	chr19:56165200-56167800	Active TSS	Aorta	Aorta
26	chr19:56165200-56167800	Active TSS	Placenta Amnion	Placenta Amnion
27	chr19:56165200-56167800	Bivalent/Poised TSS	HepG2	liver
28	chr19:56165200-56168000	Active TSS	Lung	lung
29	chr19:56165200-56168000	Active TSS	Ovary	ovary
30	chr19:56165200-56168000	Active TSS	NHDF-Ad	bronchial
31	chr19:56165200-56168200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr19:56165600-56168200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr19:56166400-56168800	Flanking Active TSS	Primary hematopoietic stem cells	blood
34	chr19:56166600-56168800	Flanking Active TSS	Primary B cells from cord blood	blood
35	chr19:56166600-56168800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr19:56166800-56168000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr19:56166800-56169400	Flanking Active TSS	Adipose Nuclei	Adipose
38	chr19:56167000-56167800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
39	chr19:56167000-56167800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
40	chr19:56167000-56167800	Flanking Active TSS	Primary B cells from peripheral blood	blood
41	chr19:56167000-56167800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
42	chr19:56167000-56167800	Flanking Active TSS	Left Ventricle	heart
43	chr19:56167000-56168000	Flanking Active TSS	Liver	Liver
44	chr19:56167000-56168200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
45	chr19:56167000-56168400	Flanking Active TSS	Fetal Brain Male	brain
46	chr19:56167000-56168400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
47	chr19:56167000-56168600	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr19:56167000-56169000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
49	chr19:56167000-56169200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
50	chr19:56167000-56169200	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--

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