Variant report

Variant	rs73054869
Chromosome Location	chr19:52193168-52193169
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	HCFC1	chr19:52193098-52193273	K562	blood:	n/a	n/a
2	ELF1	chr19:52192931-52193342	A549	lung:	n/a	chr19:52193044-52193057 chr19:52193045-52193056
3	POLR2A	chr19:52192548-52195125	HUVEC	blood vessel:	n/a	n/a
4	TBL1XR1	chr19:52193103-52194636	K562	blood:	n/a	n/a
5	ZBTB7A	chr19:52193068-52193384	HepG2	liver:	n/a	n/a
6	POLR2A	chr19:52193168-52193838	HUVEC	blood vessel:	n/a	n/a
7	RXRA	chr19:52193092-52193405	H1-hESC	embryonic stem cell:	n/a	chr19:52193241-52193261 chr19:52193244-52193257 chr19:52193239-52193255 chr19:52193244-52193257 chr19:52193244-52193257 chr19:52193243-52193259
8	MAX	chr19:52192947-52194342	A549	lung:	n/a	chr19:52193788-52193797 chr19:52194166-52194176 chr19:52193267-52193277 chr19:52194223-52194233
9	BCL3	chr19:52192898-52193378	A549	lung:	n/a	chr19:52193326-52193335 chr19:52193169-52193182 chr19:52193321-52193334
10	POLR2A	chr19:52190786-52194855	IMR90	lung:	n/a	n/a
11	HDAC2	chr19:52192957-52194324	MCF-7	breast:	n/a	n/a
12	RCOR1	chr19:52193100-52193282	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr19:52192963-52193438	A549	lung:	n/a	n/a
14	POLR2A	chr19:52191161-52194568	HUVEC	blood vessel:	n/a	n/a
15	JUND	chr19:52192947-52194697	A549	lung:	n/a	n/a
16	ETS1	chr19:52192959-52193312	A549	lung:	n/a	chr19:52193271-52193282 chr19:52193205-52193218 chr19:52193207-52193218
17	HNF4G	chr19:52193092-52193326	HepG2	liver:	n/a	chr19:52193244-52193258 chr19:52193245-52193257 chr19:52193244-52193257 chr19:52193239-52193255 chr19:52193245-52193257 chr19:52193244-52193251 chr19:52193242-52193254
18	CREB1	chr19:52192944-52193486	A549	lung:	n/a	n/a
19	MAX	chr19:52190747-52194793	A549	lung:	n/a	chr19:52192371-52192381 chr19:52193788-52193797 chr19:52194166-52194176 chr19:52193267-52193277 chr19:52192441-52192451 chr19:52194223-52194233 chr19:52192611-52192621
20	POLR2A	chr19:52192978-52193271	HCT-116	colon:	n/a	n/a
21	POLR2A	chr19:52192946-52194708	SK-N-SH	brain:	n/a	n/a
22	MAZ	chr19:52190733-52195005	IMR90	lung:	n/a	chr19:52192371-52192381 chr19:52193788-52193797 chr19:52194166-52194176 chr19:52193267-52193277 chr19:52192441-52192451 chr19:52194223-52194233 chr19:52192611-52192621
23	POLR2A	chr19:52190880-52195017	PFSK-1	brain:	n/a	n/a
24	BCL3	chr19:52191885-52194262	A549	lung:	n/a	chr19:52193326-52193335 chr19:52194168-52194181 chr19:52192591-52192604 chr19:52192366-52192379 chr19:52194169-52194178 chr19:52193878-52193887 chr19:52192370-52192383 chr19:52193169-52193182 chr19:52193321-52193334
25	SP1	chr19:52192942-52194820	H1-hESC	embryonic stem cell:	n/a	chr19:52194193-52194207 chr19:52194168-52194178 chr19:52194161-52194173 chr19:52193770-52193782 chr19:52194167-52194179 chr19:52194168-52194177 chr19:52193856-52193865 chr19:52194258-52194272 chr19:52193694-52193706 chr19:52193266-52193278 chr19:52193073-52193087 chr19:52193855-52193867 chr19:52193767-52193781 chr19:52194162-52194172 chr19:52194394-52194403 chr19:52193772-52193781 chr19:52193278-52193292 chr19:52194167-52194179 chr19:52194162-52194171 chr19:52193852-52193866 chr19:52194393-52194403 chr19:52193771-52193780 chr19:52194158-52194172 chr19:52193855-52193866 chr19:52193695-52193709 chr19:52194161-52194173 chr19:52193770-52193782 chr19:52194169-52194178 chr19:52194164-52194178 chr19:52193694-52193706 chr19:52193203-52193212
26	UBTF	chr19:52191202-52193378	K562	blood:	n/a	n/a
27	MXI1	chr19:52190804-52195103	SK-N-SH	brain:	n/a	chr19:52193788-52193803
28	NR2F2	chr19:52192973-52194396	K562	blood:	n/a	n/a
29	JUND	chr19:52192991-52194316	A549	lung:	n/a	n/a
30	POLR2A	chr19:52193161-52193373	HepG2	liver:	n/a	n/a
31	POLR2A	chr19:52190868-52194746	PFSK-1	brain:	n/a	n/a
32	REST	chr19:52190718-52193267	H1-neurons	neurons:	n/a	chr19:52192489-52192502 chr19:52192486-52192499 chr19:52192486-52192499 chr19:52192482-52192502
33	POLR2A	chr19:52192947-52193340	HUVEC	blood vessel:	n/a	n/a
34	GATA3	chr19:52192833-52194860	A549	lung:	n/a	n/a
35	PBX3	chr19:52192013-52194307	A549	lung:	n/a	chr19:52192101-52192121
36	EP300	chr19:52193122-52193386	K562	blood:	n/a	n/a
37	MYC	chr19:52193138-52193217	MCF-7	breast:	n/a	n/a
38	MYC	chr19:52193070-52193261	K562	blood:	n/a	n/a
39	REST	chr19:52192956-52193262	A549	lung:	n/a	n/a
40	CEBPD	chr19:52192960-52193390	HepG2	liver:	n/a	n/a
41	POLR2A	chr19:52191032-52194338	MCF-7	breast:	n/a	n/a
42	SIN3AK20	chr19:52193059-52194051	H1-hESC	embryonic stem cell:	n/a	n/a
43	NFIC	chr19:52193140-52194675	SK-N-SH	brain:	n/a	n/a
44	NR2F2	chr19:52193056-52193470	K562	blood:	n/a	n/a
45	HDAC2	chr19:52193000-52193369	K562	blood:	n/a	n/a
46	POLR2A	chr19:52192946-52193457	A549	lung:	n/a	n/a
47	MYC	chr19:52193068-52193316	K562	blood:	n/a	chr19:52193267-52193277
48	POLR2A	chr19:52192982-52193438	A549	lung:	n/a	n/a
49	POLR2A	chr19:52192970-52194814	U87	brain:	n/a	n/a
50	ELF1	chr19:52192963-52194312	A549	lung:	n/a	chr19:52193044-52193057 chr19:52193045-52193056

No.	Distal block	Cell Line	Cell type
1	chr19:52191310..52193737-chr19:54959271..54961784,2	MCF-7	breast:
2	chr19:52191235..52193231-chr19:52302966..52304607,2	MCF-7	breast:
3	chr19:51869555..51871818-chr19:52192464..52195337,3	MCF-7	breast:
4	chr19:52191055..52194888-chr19:52301421..52305190,4	MCF-7	breast:
5	chr19:52166500..52170915-chr19:52189684..52193816,5	MCF-7	breast:
6	chr19:52190894..52195343-chr19:52204099..52207909,11	MCF-7	breast:
7	chr19:52171940..52173838-chr19:52191282..52193363,2	MCF-7	breast:
8	chr19:52192175..52194202-chr19:52301235..52302921,2	MCF-7	breast:
9	chr19:52191148..52193451-chr19:52208033..52210074,2	MCF-7	breast:
10	chr19:52191800..52194773-chr19:52195976..52198030,3	K562	blood:
11	chr19:52192066..52193660-chr19:52283404..52285811,2	MCF-7	breast:

Variant related genes	Relation type
MIRLET7E	TF binding region
MIR125A	TF binding region
SPACA6P	TF binding region
ENSG00000273318	TF binding region
MIR99B	TF binding region
ENSG00000238486	Chromatin interaction
ENSG00000182310	Chromatin interaction
ENSG00000226696	Chromatin interaction
ENSG00000269959	Chromatin interaction
ENSG00000273318	Chromatin interaction
ENSG00000198972	Chromatin interaction
ENSG00000167615	Chromatin interaction
ENSG00000208008	Chromatin interaction
ENSG00000105379	Chromatin interaction
ENSG00000160318	Chromatin interaction
ENSG00000269403	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10408866	1.00[ASN][1000 genomes]
rs10422427	1.00[ASN][1000 genomes]
rs11882295	1.00[ASN][1000 genomes]
rs12459772	1.00[ASN][1000 genomes]
rs12984389	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1868940	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28556823	1.00[ASN][1000 genomes]
rs2902883	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34817696	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55977254	1.00[ASN][1000 genomes]
rs57048628	1.00[ASN][1000 genomes]
rs58044915	1.00[ASN][1000 genomes]
rs59294761	1.00[ASN][1000 genomes]
rs62106911	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8109047	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758504	chr19:51991896-52266700	Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	542 gene(s)	inside rSNPs	diseases
2	esv2758767	chr19:51991896-52604625	Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	578 gene(s)	inside rSNPs	diseases
3	nsv482909	chr19:52091735-52266700	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	533 gene(s)	inside rSNPs	diseases
4	nsv1064914	chr19:52103914-52231564	Transcr. at gene 5' and 3' Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	529 gene(s)	inside rSNPs	diseases
5	nsv544052	chr19:52103914-52271247	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	531 gene(s)	inside rSNPs	diseases
6	nsv1056825	chr19:52103914-52359815	Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	541 gene(s)	inside rSNPs	diseases
7	nsv544053	chr19:52103914-52359815	ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	541 gene(s)	inside rSNPs	diseases
8	nsv1065410	chr19:52103914-52889530	Genic enhancers Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS 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 miRNA miRNA target site	596 gene(s)	inside rSNPs	diseases
9	esv1843680	chr19:52131510-52211749	Active TSS Flanking Active TSS Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	525 gene(s)	inside rSNPs	diseases
10	nsv1066046	chr19:52147399-52271247	Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	525 gene(s)	inside rSNPs	diseases
11	nsv544054	chr19:52147399-52271247	Active TSS Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	525 gene(s)	inside rSNPs	diseases
12	nsv912296	chr19:52182363-52231032	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats 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 miRNA	518 gene(s)	inside rSNPs	diseases
13	nsv915725	chr19:52184488-52439676	Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	541 gene(s)	inside rSNPs	diseases
14	nsv9742	chr19:52187538-52221742	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	517 gene(s)	inside rSNPs	diseases
15	esv3371725	chr19:52192115-52194388	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52190400-52194600	Active TSS	Fetal Brain Female	brain
2	chr19:52190800-52194400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr19:52190800-52194400	Active TSS	HUES6 Cell Line	embryonic stem cell
4	chr19:52190800-52194800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr19:52190800-52194800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr19:52190800-52195000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr19:52190800-52195000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr19:52190800-52195200	Active TSS	H9 Cell Line	embryonic stem cell
9	chr19:52191000-52193400	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
10	chr19:52191000-52194000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
11	chr19:52191000-52194600	Active TSS	Psoas Muscle	Psoas
12	chr19:52191000-52194600	Active TSS	A549	lung
13	chr19:52191000-52195200	Active TSS	iPS-15b Cell Line	embryonic stem cell
14	chr19:52191000-52195400	Active TSS	HUES64 Cell Line	embryonic stem cell
15	chr19:52191000-52195800	Active TSS	Pancreatic Islets	Pancreatic Islet
16	chr19:52191200-52193600	Active TSS	Hela-S3	cervix
17	chr19:52191200-52194800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr19:52191200-52194800	Active TSS	Left Ventricle	heart
19	chr19:52191200-52195000	Active TSS	ES-I3 Cell Line	embryonic stem cell
20	chr19:52191200-52195000	Active TSS	Ovary	ovary
21	chr19:52191200-52196200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr19:52191200-52196200	Active TSS	Fetal Kidney	kidney
23	chr19:52191400-52193400	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
24	chr19:52191400-52194400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr19:52191400-52194600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
26	chr19:52191400-52194600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr19:52191400-52194600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
28	chr19:52191400-52194800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr19:52191400-52194800	Active TSS	Aorta	Aorta
30	chr19:52191400-52195000	Active TSS	HUES48 Cell Line	embryonic stem cell
31	chr19:52191400-52195200	Active TSS	H1 Cell Line	embryonic stem cell
32	chr19:52191400-52195400	Active TSS	HSMMtube	muscle
33	chr19:52191600-52193600	Active TSS	Brain Germinal Matrix	brain
34	chr19:52191600-52194200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr19:52191600-52194400	Active TSS	Brain Inferior Temporal Lobe	brain
36	chr19:52191600-52194400	Active TSS	Brain Substantia Nigra	brain
37	chr19:52191600-52194400	Active TSS	NHEK	skin
38	chr19:52191600-52194600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr19:52191600-52194600	Active TSS	Brain Angular Gyrus	brain
40	chr19:52191600-52194600	Active TSS	Brain Cingulate Gyrus	brain
41	chr19:52191600-52194800	Active TSS	Breast Myoepithelial Primary Cells	Breast
42	chr19:52191600-52194800	Active TSS	Esophagus	oesophagus
43	chr19:52191600-52194800	Active TSS	HSMM	muscle
44	chr19:52191600-52195000	Active TSS	Placenta Amnion	Placenta Amnion
45	chr19:52191600-52195200	Active TSS	iPS-20b Cell Line	embryonic stem cell
46	chr19:52191600-52195200	Active TSS	Colon Smooth Muscle	Colon
47	chr19:52191600-52195200	Active TSS	Rectal Smooth Muscle	rectum
48	chr19:52191800-52193200	Active TSS	Duodenum Smooth Muscle	Duodenum
49	chr19:52191800-52193600	Active TSS	Fetal Brain Male	brain
50	chr19:52191800-52193800	Bivalent Enhancer	Primary B cells from peripheral blood	blood

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