Variant report

Variant	rs73932080
Chromosome Location	chr19:42250851-42250852
allele	A/G
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	CTCF	chr19:42250760-42250910	HFF-Myc	foreskin:	n/a	n/a
2	RAD21	chr19:42250356-42251089	A549	lung:	n/a	chr19:42250722-42250741
3	CTCF	chr19:42250641-42250868	MCF-7	breast:	n/a	chr19:42250724-42250742 chr19:42250719-42250740
4	CTCF	chr19:42250591-42250889	GM12878	blood:	n/a	chr19:42250724-42250742 chr19:42250719-42250740
5	SMC3	chr19:42250543-42250920	Hela-S3	cervix:	n/a	chr19:42250726-42250740
6	SMC3	chr19:42250599-42250852	K562	blood:	n/a	chr19:42250726-42250740
7	CTCF	chr19:42250517-42250860	A549	lung:	n/a	chr19:42250724-42250742 chr19:42250719-42250740
8	CTCF	chr19:42250523-42250902	ECC-1	luminal epithelium:	n/a	chr19:42250724-42250742 chr19:42250719-42250740
9	CTCF	chr19:42250613-42250883	K562	blood:	n/a	chr19:42250724-42250742 chr19:42250719-42250740
10	CTCF	chr19:42250569-42250881	HepG2	liver:	n/a	chr19:42250724-42250742 chr19:42250719-42250740
11	CTCF	chr19:42250556-42250923	K562	blood:	n/a	chr19:42250724-42250742 chr19:42250719-42250740
12	RAD21	chr19:42250556-42250908	HepG2	liver:	n/a	chr19:42250722-42250741
13	CTCF	chr19:42250641-42250855	Fibrobl	skin:	n/a	chr19:42250724-42250742 chr19:42250719-42250740
14	CTCF	chr19:42250618-42250869	GM19240	blood:	n/a	chr19:42250724-42250742 chr19:42250719-42250740
15	RAD21	chr19:42250573-42250922	SK-N-SH_RA	brain:	n/a	chr19:42250722-42250741
16	SMC3	chr19:42250590-42250901	GM12878	blood:	n/a	chr19:42250726-42250740
17	CTCF	chr19:42250614-42250852	Hela-S3	cervix:	n/a	chr19:42250724-42250742 chr19:42250719-42250740
18	CTCF	chr19:42250640-42250870	GM12867	blood:	n/a	chr19:42250724-42250742 chr19:42250719-42250740
19	CTCF	chr19:42250612-42250851	Pancreas_OC	pancreas:	n/a	chr19:42250724-42250742 chr19:42250719-42250740
20	CTCF	chr19:42250614-42250851	HUVEC	blood vessel:	n/a	chr19:42250724-42250742 chr19:42250719-42250740
21	RAD21	chr19:42250553-42250911	A549	lung:	n/a	chr19:42250722-42250741
22	RAD21	chr19:42250486-42250970	MCF-7	breast:	n/a	chr19:42250722-42250741
23	RAD21	chr19:42250559-42250910	IMR90	lung:	n/a	chr19:42250722-42250741
24	RAD21	chr19:42250539-42250894	GM12878	blood:	n/a	chr19:42250722-42250741
25	ZKSCAN1	chr19:42250678-42250853	Hela-S3	cervix:	n/a	n/a
26	CTCF	chr19:42250504-42250924	A549	lung:	n/a	chr19:42250724-42250742 chr19:42250719-42250740
27	CTCF	chr19:42250483-42250955	MCF-7	breast:	n/a	chr19:42250724-42250742 chr19:42250719-42250740
28	RAD21	chr19:42250528-42250954	ECC-1	luminal epithelium:	n/a	chr19:42250722-42250741
29	CTCF	chr19:42250627-42250886	GM12892	blood:	n/a	chr19:42250724-42250742 chr19:42250719-42250740
30	CTCF	chr19:42250435-42251031	HCT-116	colon:	n/a	chr19:42250724-42250742 chr19:42250719-42250740
31	CTCF	chr19:42250720-42250870	HFF	foreskin:	n/a	chr19:42250724-42250742
32	RAD21	chr19:42250550-42250915	K562	blood:	n/a	chr19:42250722-42250741
33	RAD21	chr19:42250472-42250898	HepG2	liver:	n/a	chr19:42250722-42250741
34	CTCF	chr19:42250638-42250863	LNCaP	prostate:	n/a	chr19:42250724-42250742 chr19:42250719-42250740
35	CTCF	chr19:42250720-42250870	HMEC	breast:	n/a	chr19:42250724-42250742
36	CTCF	chr19:42250541-42250917	GM12878	blood:	n/a	chr19:42250724-42250742 chr19:42250719-42250740
37	CTCF	chr19:42250626-42250883	GM19238	blood:	n/a	chr19:42250724-42250742 chr19:42250719-42250740
38	RAD21	chr19:42250515-42251049	HCT-116	colon:	n/a	chr19:42250722-42250741
39	CTCF	chr19:42250654-42250885	GM12891	blood:	n/a	chr19:42250724-42250742 chr19:42250719-42250740
40	CTCF	chr19:42250450-42250937	A549	lung:	n/a	chr19:42250724-42250742 chr19:42250719-42250740
41	RAD21	chr19:42250465-42250972	HCT-116	colon:	n/a	chr19:42250722-42250741
42	CTCF	chr19:42250638-42250856	GM10248	blood:	n/a	chr19:42250724-42250742 chr19:42250719-42250740
43	FOXP2	chr19:42250592-42250913	SK-N-MC	brain:	n/a	n/a
44	CTCF	chr19:42250740-42250890	A549	lung:	n/a	n/a
45	CTCF	chr19:42250434-42250992	MCF-7	breast:	n/a	chr19:42250724-42250742 chr19:42250719-42250740
46	CTCF	chr19:42250720-42250870	MCF-7	breast:	n/a	chr19:42250724-42250742
47	RAD21	chr19:42250327-42251032	MCF-7	breast:	n/a	chr19:42250722-42250741
48	CTCF	chr19:42250760-42250910	WI-38	lung:	n/a	n/a
49	CTCF	chr19:42250519-42250947	K562	blood:	n/a	chr19:42250724-42250742 chr19:42250719-42250740
50	CTCF	chr19:42250638-42250886	GM19239	blood:	n/a	chr19:42250724-42250742 chr19:42250719-42250740

No.	Distal block	Cell Line	Cell type
1	chr19:42212037..42212962-chr19:42250295..42251188,4	MCF-7	breast:
2	chr19:42250749..42252304-chr19:42286973..42289582,3	MCF-7	breast:
3	chr19:42209137..42209823-chr19:42250235..42251244,3	MCF-7	breast:
4	chr19:42250343..42251080-chr19:42288592..42289100,2	MCF-7	breast:
5	chr19:42211491..42212027-chr19:42250292..42251139,2	K562	blood:
6	chr19:42147964..42148906-chr19:42250000..42251190,4	MCF-7	breast:
7	chr19:42209556..42212105-chr19:42250130..42251602,39	MCF-7	breast:
8	chr19:42147220..42149633-chr19:42250736..42252324,3	MCF-7	breast:
9	chr19:42210648..42213513-chr19:42249142..42252570,4	MCF-7	breast:
10	chr19:42210533..42211382-chr19:42250275..42251260,3	K562	blood:
11	chr19:42249789..42252137-chr19:42296229..42297905,2	MCF-7	breast:
12	chr19:42238634..42240225-chr19:42250463..42251967,2	MCF-7	breast:
13	chr19:42148303..42148992-chr19:42250108..42251260,4	K562	blood:
14	chr19:42210030..42211723-chr19:42249785..42251642,16	MCF-7	breast:

Variant related genes	Relation type
CEACAM6	TF binding region
ENSG00000105388	Chromatin interaction
ENSG00000007306	Chromatin interaction
ENSG00000267881	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs56777717	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58127675	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59623589	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59675676	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61325364	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6508994	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6508995	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7249202	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7249254	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7249385	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7249444	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7251260	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7255583	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7256339	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7257822	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73932049	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73932050	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73932052	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73932056	1.00[AMR][1000 genomes]
rs73932057	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73932064	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73932065	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73932066	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73932084	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73932085	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73932087	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73932088	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9749010	0.82[AFR][1000 genomes];1.00[AMR][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	nsv522854	chr19:42120283-42931004	Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	esv3425986	chr19:42212540-42259719	Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv579615	chr19:42221434-42310388	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	esv3430577	chr19:42247653-42285973	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv911774	chr19:42250325-42288821	Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42246600-42251000	Enhancers	Primary hematopoietic stem cells short term culture	blood
2	chr19:42247000-42251000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr19:42248200-42251000	Enhancers	Fetal Intestine Small	intestine
4	chr19:42249000-42251200	Enhancers	Stomach Mucosa	stomach
5	chr19:42249400-42251000	Enhancers	Rectal Mucosa Donor 29	rectum
6	chr19:42250400-42251200	Enhancers	Primary hematopoietic stem cells	blood
7	chr19:42250600-42251000	Bivalent Enhancer	Primary B cells from cord blood	blood
8	chr19:42250600-42251000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr19:42250600-42251000	Bivalent Enhancer	A549	lung
10	chr19:42250600-42252400	Weak transcription	Colonic Mucosa	Colon
11	chr19:42250800-42251000	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
12	chr19:42250800-42251000	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
13	chr19:42250800-42251000	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
14	chr19:42250800-42251000	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
15	chr19:42250800-42251000	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
16	chr19:42250800-42251000	Bivalent Enhancer	Duodenum Mucosa	Duodenum
17	chr19:42250800-42251000	Enhancers	Pancreas	Pancrea
18	chr19:42250800-42251200	Bivalent Enhancer	Rectal Mucosa Donor 31	rectum
19	chr19:42250800-42251400	Enhancers	Esophagus	oesophagus
20	chr19:42250800-42253200	Enhancers	Primary neutrophils fromperipheralblood	blood

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