Variant report

Variant	rs7257231
Chromosome Location	chr19:45252439-45252440
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	chr19:45251911-45252476	A549	lung:	n/a	n/a
2	ZBTB7A	chr19:45251582-45252457	K562	blood:	n/a	n/a
3	JUND	chr19:45250219-45252555	A549	lung:	n/a	chr19:45250880-45250887 chr19:45252543-45252552 chr19:45250877-45250888 chr19:45252545-45252554 chr19:45250716-45250724 chr19:45250875-45250886 chr19:45252546-45252555 chr19:45252542-45252551 chr19:45250879-45250887 chr19:45250845-45250854 chr19:45250879-45250887 chr19:45252544-45252553
4	ZBTB7A	chr19:45250531-45252587	ECC-1	luminal epithelium:	n/a	n/a
5	MAX	chr19:45249618-45252538	A549	lung:	n/a	chr19:45250878-45250887
6	POLR2A	chr19:45251701-45252458	A549	lung:	n/a	n/a
7	CHD1	chr19:45251912-45252484	GM12878	blood:	n/a	n/a
8	CHD1	chr19:45250110-45253686	IMR90	lung:	n/a	chr19:45251838-45251848
9	BCL3	chr19:45248078-45253687	A549	lung:	n/a	chr19:45248561-45248574 chr19:45250739-45250752 chr19:45248567-45248580 chr19:45250771-45250780
10	EBF1	chr19:45250136-45252561	GM12878	blood:	n/a	chr19:45250505-45250516 chr19:45250756-45250765 chr19:45252399-45252408
11	ZBTB7A	chr19:45251480-45252454	K562	blood:	n/a	n/a
12	POLR2A	chr19:45251877-45253521	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr19:45249872-45253681	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr19:45252236-45253600	U87	brain:	n/a	n/a
15	TFAP2C	chr19:45250383-45252694	Hela-S3	cervix:	n/a	n/a
16	PML	chr19:45251327-45252458	GM12878	blood:	n/a	chr19:45252393-45252401
17	RELA	chr19:45250246-45252444	GM12891	blood:	n/a	chr19:45250772-45250781 chr19:45250772-45250781
18	POLR2A	chr19:45252292-45253527	A549	lung:	n/a	n/a
19	TCF12	chr19:45247727-45253774	A549	lung:	n/a	chr19:45248399-45248407 chr19:45249956-45249966
20	ZBTB7A	chr19:45251366-45252546	ECC-1	luminal epithelium:	n/a	n/a
21	POLR2A	chr19:45250698-45252463	HepG2	liver:	n/a	n/a
22	POLR2A	chr19:45252259-45253459	U87	brain:	n/a	n/a
23	MAZ	chr19:45249597-45253664	IMR90	lung:	n/a	chr19:45252537-45252546 chr19:45250878-45250887 chr19:45252540-45252550
24	POLR2A	chr19:45252230-45253606	U87	brain:	n/a	n/a
25	POLR2A	chr19:45252276-45252740	Hela-S3	cervix:	n/a	n/a
26	BCLAF1	chr19:45251705-45252515	GM12878	blood:	n/a	n/a
27	BCL3	chr19:45247680-45253680	A549	lung:	n/a	chr19:45248561-45248574 chr19:45250739-45250752 chr19:45248567-45248580 chr19:45250771-45250780
28	POLR2A	chr19:45250730-45252538	GM18505	blood:	n/a	n/a
29	POLR2A	chr19:45251697-45252546	PANC-1	pancreas:	n/a	n/a
30	POLR2A	chr19:45250510-45252468	HUVEC	blood vessel:	n/a	n/a
31	POLR2A	chr19:45250394-45253526	Hela-S3	cervix:	n/a	n/a
32	TFAP2A	chr19:45250384-45252473	Hela-S3	cervix:	n/a	chr19:45250640-45250652 chr19:45250640-45250652 chr19:45251863-45251877 chr19:45250640-45250652 chr19:45251863-45251877 chr19:45250640-45250652 chr19:45251863-45251877
33	POLR2A	chr19:45252410-45253639	GM12878	blood:	n/a	n/a
34	RCOR1	chr19:45252361-45253668	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:45164861..45166953-chr19:45250378..45253353,2	MCF-7	breast:
2	chr19:45252359..45252902-chr9:34179841..34180546,2	Hela-S3	cervix:
3	chr19:45150946..45153817-chr19:45251773..45254167,2	MCF-7	breast:
4	chr19:45251797..45254336-chr19:45349633..45353327,3	K562	blood:
5	chr19:45173518..45176542-chr19:45249418..45252711,3	MCF-7	breast:
6	chr19:45250646..45253385-chr19:45348787..45352398,5	MCF-7	breast:
7	chr19:45180699..45183749-chr19:45249057..45252629,3	MCF-7	breast:
8	chr19:45249129..45253567-chr19:45309146..45313529,6	MCF-7	breast:
9	chr19:45250044..45254049-chr19:45347224..45351011,6	MCF-7	breast:
10	chr19:45250785..45254453-chr19:45309921..45313662,4	MCF-7	breast:
11	chr17:79936078..79936868-chr19:45251918..45252553,2	Hela-S3	cervix:
12	chr19:45252053..45254233-chr19:45351379..45354120,2	MCF-7	breast:
13	chr19:45252003..45254960-chr19:45323071..45325536,2	K562	blood:
14	chr19:45198197..45200350-chr19:45252403..45254162,3	K562	blood:
15	chr19:45222394..45233722-chr19:45248498..45258065,33	MCF-7	breast:
16	chr16:75682151..75683053-chr19:45252133..45253014,2	Hela-S3	cervix:

Variant related genes	Relation type
BCL3	TF binding region
ENSG00000166848	Chromatin interaction
ENSG00000073008	Chromatin interaction
ENSG00000186567	Chromatin interaction
ENSG00000187244	Chromatin interaction
ENSG00000130202	Chromatin interaction
ENSG00000252200	Chromatin interaction
ENSG00000065427	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs17658713	0.80[EUR][1000 genomes]
rs17728272	0.82[EUR][1000 genomes]
rs4803749	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59170622	0.82[EUR][1000 genomes]
rs8100197	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912116	chr19:45146103-45298069	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
2	nsv833841	chr19:45208486-45308043	Enhancers Bivalent/Poised TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
3	esv3335183	chr19:45225161-45253316	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	esv3324918	chr19:45250737-45253285	Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	esv3447789	chr19:45251012-45253160	Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:45249800-45253200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
2	chr19:45250200-45252800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
3	chr19:45250200-45252800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
4	chr19:45250200-45252800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
5	chr19:45250400-45252600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
6	chr19:45250400-45252600	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr19:45250400-45252600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
8	chr19:45250400-45252800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr19:45250400-45252800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr19:45250400-45252800	Active TSS	Psoas Muscle	Psoas
11	chr19:45250400-45253200	Active TSS	Brain Inferior Temporal Lobe	brain
12	chr19:45250400-45254000	Active TSS	Sigmoid Colon	Sigmoid Colon
13	chr19:45250600-45252600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
14	chr19:45250600-45252600	Active TSS	Colon Smooth Muscle	Colon
15	chr19:45250600-45252600	Active TSS	Placenta Amnion	Placenta Amnion
16	chr19:45250600-45252600	Active TSS	Rectal Smooth Muscle	rectum
17	chr19:45250600-45252800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
18	chr19:45250600-45252800	Active TSS	Duodenum Mucosa	Duodenum
19	chr19:45250600-45253000	Active TSS	Right Ventricle	heart
20	chr19:45250600-45253000	Active TSS	HSMM	muscle
21	chr19:45250600-45253200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr19:45250600-45253200	Active TSS	Liver	Liver
23	chr19:45250600-45253200	Active TSS	Fetal Kidney	kidney
24	chr19:45250600-45253200	Active TSS	Left Ventricle	heart
25	chr19:45250600-45253200	Active TSS	Ovary	ovary
26	chr19:45250600-45253200	Active TSS	Right Atrium	heart
27	chr19:45250600-45253200	Active TSS	NHLF	lung
28	chr19:45250600-45253400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr19:45250600-45253400	Active TSS	Pancreatic Islets	Pancreatic Islet
30	chr19:45250800-45252600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr19:45250800-45253000	Active TSS	A549	lung
32	chr19:45250800-45253200	Active TSS	Brain Angular Gyrus	brain
33	chr19:45250800-45253200	Active TSS	Esophagus	oesophagus
34	chr19:45251000-45252800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr19:45251000-45253000	Active TSS	Aorta	Aorta
36	chr19:45251000-45253000	Active TSS	Spleen	Spleen
37	chr19:45251000-45253200	Active TSS	Lung	lung
38	chr19:45251000-45253400	Active TSS	Small Intestine	intestine
39	chr19:45251200-45252600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr19:45251200-45253200	Active TSS	Pancreas	Pancrea
41	chr19:45251400-45252800	Active TSS	Monocytes-CD14+_RO01746	blood
42	chr19:45251600-45252600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr19:45251600-45252600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr19:45251600-45252600	Active TSS	Primary hematopoietic stem cells short term culture	blood
45	chr19:45251600-45252600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
46	chr19:45251600-45252600	Active TSS	Primary T regulatory cells fromperipheralblood	blood
47	chr19:45251600-45252600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
48	chr19:45251600-45252600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr19:45251600-45252600	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr19:45251600-45252600	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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