Variant report

Variant	rs11671749
Chromosome Location	chr19:23457072-23457073
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	TAF1	chr19:23456162-23457343	H1-hESC	embryonic stem cell:	n/a	n/a
2	BHLHE40	chr19:23456780-23457323	GM12878	blood:	n/a	n/a
3	ELF1	chr19:23456886-23457260	HepG2	liver:	n/a	chr19:23457047-23457060 chr19:23457014-23457026
4	POLR2A	chr19:23456460-23457301	MCF-7	breast:	n/a	n/a
5	RUNX3	chr19:23456619-23457311	GM12878	blood:	n/a	n/a
6	POLR2A	chr19:23456522-23457278	PFSK-1	brain:	n/a	n/a
7	POLR2A	chr19:23456453-23457230	GM12878	blood:	n/a	n/a
8	POLR2A	chr19:23456737-23457234	PANC-1	pancreas:	n/a	n/a
9	POLR2A	chr19:23456406-23457369	GM12892	blood:	n/a	n/a
10	POLR2A	chr19:23456774-23457078	A549	lung:	n/a	n/a
11	IRF3	chr19:23456858-23457175	GM12878	blood:	n/a	chr19:23457055-23457069
12	JUND	chr19:23456703-23457311	H1-hESC	embryonic stem cell:	n/a	n/a
13	YY1	chr19:23456316-23457211	H1-hESC	embryonic stem cell:	n/a	chr19:23456729-23456751 chr19:23456716-23456730 chr19:23456730-23456738 chr19:23456717-23456731 chr19:23456729-23456739 chr19:23456728-23456740
14	POLR2A	chr19:23456537-23457181	HL-60	blood:	n/a	n/a
15	TAF1	chr19:23456829-23457177	GM12891	blood:	n/a	n/a
16	MYC	chr19:23456586-23457232	NB4	blood:	n/a	n/a
17	EBF1	chr19:23456981-23457319	GM12878	blood:	n/a	n/a
18	TAF1	chr19:23456538-23457228	SK-N-SH	brain:	n/a	n/a
19	MAFK	chr19:23456865-23457161	HepG2	liver:	n/a	n/a
20	TCF3	chr19:23456897-23457084	GM12878	blood:	n/a	n/a
21	GTF2F1	chr19:23456578-23457221	H1-hESC	embryonic stem cell:	n/a	n/a
22	RELA	chr19:23456506-23457340	GM18505	blood:	n/a	n/a
23	PML	chr19:23456767-23457282	MCF-7	breast:	n/a	n/a
24	ELF1	chr19:23456682-23457338	MCF-7	breast:	n/a	chr19:23457047-23457060 chr19:23456718-23456730 chr19:23457014-23457026
25	TAF1	chr19:23456303-23457281	H1-neurons	neurons:	n/a	n/a
26	ELF1	chr19:23456802-23457291	HepG2	liver:	n/a	chr19:23457047-23457060 chr19:23457014-23457026
27	ELF1	chr19:23456534-23457214	GM12878	blood:	n/a	chr19:23457047-23457060 chr19:23456718-23456730 chr19:23457014-23457026
28	POLR2A	chr19:23456514-23457308	GM10847	blood:	n/a	n/a
29	SIN3AK20	chr19:23456567-23457299	SK-N-SH	brain:	n/a	n/a
30	POLR2A	chr19:23456596-23457273	Gliobla	brain:	n/a	n/a
31	NRF1	chr19:23456849-23457257	GM12878	blood:	n/a	chr19:23457086-23457100
32	POLR2A	chr19:23456611-23457165	A549	lung:	n/a	n/a
33	POLR2A	chr19:23456581-23457200	HEK293	kidney:	n/a	n/a
34	POLR2A	chr19:23456720-23457278	SK-N-MC	brain:	n/a	n/a
35	E2F4	chr19:23456835-23457248	MCF10A-Er-Src	breast:	n/a	n/a
36	YY1	chr19:23456171-23457267	HepG2	liver:	n/a	chr19:23456729-23456751 chr19:23456716-23456730 chr19:23456730-23456738 chr19:23456717-23456731 chr19:23456729-23456739 chr19:23456728-23456740
37	POLR2A	chr19:23456287-23457281	H1-neurons	neurons:	n/a	n/a
38	HA-E2F1	chr19:23456606-23457300	MCF-7	breast:	n/a	n/a
39	USF2	chr19:23456567-23457223	H1-hESC	embryonic stem cell:	n/a	chr19:23456707-23456723 chr19:23456715-23456731
40	CEBPD	chr19:23456745-23457154	HepG2	liver:	n/a	n/a
41	POLR2A	chr19:23456459-23457267	GM12891	blood:	n/a	n/a
42	POLR2A	chr19:23456427-23457331	GM15510	blood:	n/a	n/a
43	POU2F2	chr19:23456800-23457191	GM12891	blood:	n/a	n/a
44	WRNIP1	chr19:23456908-23457352	GM12878	blood:	n/a	n/a
45	POLR2A	chr19:23456627-23457269	HUVEC	blood vessel:	n/a	n/a
46	YY1	chr19:23456157-23457254	SK-N-SH_RA	brain:	n/a	chr19:23456729-23456751 chr19:23456716-23456730 chr19:23456730-23456738 chr19:23456717-23456731 chr19:23456729-23456739 chr19:23456728-23456740
47	POLR2A	chr19:23456513-23457331	GM18951	blood:	n/a	n/a
48	SIN3AK20	chr19:23456993-23457258	H1-hESC	embryonic stem cell:	n/a	n/a
49	POLR2A	chr19:23456820-23457138	A549	lung:	n/a	n/a
50	YY1	chr19:23456453-23457178	NT2-D1	testis:	n/a	chr19:23456729-23456751 chr19:23456716-23456730 chr19:23456730-23456738 chr19:23456717-23456731 chr19:23456729-23456739 chr19:23456728-23456740

No.	Distal block	Cell Line	Cell type
1	chr19:23433051..23435448-chr19:23455541..23457705,2	MCF-7	breast:
2	chr19:23443599..23446084-chr19:23455345..23457112,3	MCF-7	breast:
3	chr19:23456603..23457127-chr19:24215859..24216611,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000213971	TF binding region
ENSG00000269107	TF binding region
ENSG00000196081	Chromatin interaction
ENSG00000213096	Chromatin interaction
ENSG00000268362	Chromatin interaction
ENSG00000213971	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10410090	0.81[ASN][1000 genomes]
rs10417601	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10419448	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12980365	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34237656	0.86[ASN][1000 genomes]
rs34370967	0.81[ASN][1000 genomes]
rs34465745	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34510793	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34870613	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62124083	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34470	chr19:22922549-23659458	ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	80 gene(s)	inside rSNPs	diseases
2	esv34907	chr19:22922549-23683097	Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	80 gene(s)	inside rSNPs	diseases
3	nsv9686	chr19:22989454-23653750	Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	76 gene(s)	inside rSNPs	diseases
4	nsv817826	chr19:23000745-23620632	Active TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	75 gene(s)	inside rSNPs	diseases
5	esv3693269	chr19:23000745-23652839	Weak transcription Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	76 gene(s)	inside rSNPs	diseases
6	esv2758491	chr19:23071299-23940467	ZNF genes & repeats Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	87 gene(s)	inside rSNPs	diseases
7	nsv1065157	chr19:23091826-23812323	Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	83 gene(s)	inside rSNPs	diseases
8	nsv543959	chr19:23091826-23812323	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	83 gene(s)	inside rSNPs	diseases
9	esv3424935	chr19:23111817-23495542	Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
10	esv3429878	chr19:23246650-23590744	Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
11	esv3410568	chr19:23246670-23590714	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
12	esv3433243	chr19:23249108-23585814	Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
13	esv3387823	chr19:23265885-23590028	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
14	esv3321838	chr19:23303462-23482478	Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
15	nsv833789	chr19:23329463-23487797	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
16	esv3440847	chr19:23361380-23481908	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
17	esv3446056	chr19:23361400-23481878	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
18	nsv579033	chr19:23387788-23461424	Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
19	nsv579034	chr19:23387788-23610784	ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
20	nsv833790	chr19:23405972-23557520	ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
21	esv3332495	chr19:23451842-23598069	Active TSS Strong transcription ZNF genes & repeats Genic enhancers Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
22	esv3319024	chr19:23456003-23598068	Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
23	esv3319025	chr19:23456003-23598068	Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:23454800-23457400	Active TSS	Fetal Brain Female	brain
2	chr19:23455000-23457600	Active TSS	Breast Myoepithelial Primary Cells	Breast
3	chr19:23455200-23457400	Active TSS	H1 Cell Line	embryonic stem cell
4	chr19:23455200-23457400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr19:23455200-23457600	Active TSS	Brain Inferior Temporal Lobe	brain
6	chr19:23455400-23457200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr19:23455400-23457800	Active TSS	HUES6 Cell Line	embryonic stem cell
8	chr19:23455600-23457200	Active TSS	iPS-18 Cell Line	embryonic stem cell
9	chr19:23455600-23457200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr19:23455600-23457200	Active TSS	Primary T cells fromperipheralblood	blood
11	chr19:23455600-23457200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr19:23455600-23457200	Active TSS	Fetal Kidney	kidney
13	chr19:23455600-23457200	Active TSS	Stomach Smooth Muscle	stomach
14	chr19:23455600-23457400	Active TSS	H9 Cell Line	embryonic stem cell
15	chr19:23455600-23457400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr19:23455600-23457400	Active TSS	Brain Substantia Nigra	brain
17	chr19:23455600-23457400	Active TSS	Fetal Brain Male	brain
18	chr19:23455600-23457400	Active TSS	Thymus	Thymus
19	chr19:23455600-23457400	Active TSS	NHDF-Ad	bronchial
20	chr19:23455600-23457600	Active TSS	ES-I3 Cell Line	embryonic stem cell
21	chr19:23455600-23457600	Active TSS	Brain Cingulate Gyrus	brain
22	chr19:23455600-23457600	Active TSS	Fetal Intestine Small	intestine
23	chr19:23455600-23457600	Active TSS	Pancreatic Islets	Pancreatic Islet
24	chr19:23455600-23457600	Active TSS	Ovary	ovary
25	chr19:23455600-23457600	Active TSS	Psoas Muscle	Psoas
26	chr19:23455600-23457600	Active TSS	Rectal Mucosa Donor 29	rectum
27	chr19:23455600-23457600	Active TSS	Rectal Smooth Muscle	rectum
28	chr19:23455800-23457200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr19:23455800-23457200	Active TSS	iPS-20b Cell Line	embryonic stem cell
30	chr19:23455800-23457200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr19:23455800-23457200	Active TSS	Primary T killer naive cells fromperipheralblood	blood
32	chr19:23455800-23457200	Active TSS	Muscle Satellite Cultured Cells	--
33	chr19:23455800-23457400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr19:23455800-23457400	Active TSS	iPS-15b Cell Line	embryonic stem cell
35	chr19:23455800-23457400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr19:23455800-23457400	Active TSS	Primary T killer memory cells from peripheral blood	blood
37	chr19:23455800-23457400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr19:23455800-23457400	Active TSS	Brain Anterior Caudate	brain
39	chr19:23455800-23457400	Active TSS	Brain Hippocampus Middle	brain
40	chr19:23455800-23457400	Active TSS	Fetal Intestine Large	intestine
41	chr19:23455800-23457400	Active TSS	Fetal Stomach	stomach
42	chr19:23455800-23457400	Active TSS	Fetal Thymus	thymus
43	chr19:23455800-23457400	Active TSS	HMEC	breast
44	chr19:23455800-23457400	Active TSS	HSMM	muscle
45	chr19:23455800-23457400	Active TSS	NH-A	brain
46	chr19:23455800-23457400	Active TSS	NHLF	lung
47	chr19:23455800-23457600	Active TSS	HUES64 Cell Line	embryonic stem cell
48	chr19:23455800-23457600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr19:23455800-23457600	Active TSS	Colonic Mucosa	Colon
50	chr19:23455800-23457600	Active TSS	Duodenum Smooth Muscle	Duodenum

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