Variant report

Variant	rs2659061
Chromosome Location	chr19:51306793-51306794
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	POLR2A	chr19:51306598-51307510	HepG2	liver:	n/a	n/a
2	POLR2A	chr19:51305171-51308575	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr19:51306345-51308647	HL-60	blood:	n/a	n/a
4	BCL3	chr19:51306668-51308338	A549	lung:	n/a	chr19:51307558-51307571 chr19:51307558-51307567 chr19:51307959-51307968 chr19:51307280-51307289
5	POLR2A	chr19:51305218-51308754	SK-N-MC	brain:	n/a	n/a
6	POLR2A	chr19:51306504-51306846	GM12878	blood:	n/a	n/a
7	POLR2A	chr19:51306780-51306813	MCF-7	breast:	n/a	n/a
8	MXI1	chr19:51306560-51308750	IMR90	lung:	n/a	chr19:51308329-51308338 chr19:51308331-51308340
9	POLR2A	chr19:51305213-51308097	GM12892	blood:	n/a	n/a
10	POLR2A	chr19:51306721-51308607	GM12892	blood:	n/a	n/a
11	POLR2A	chr19:51305850-51308510	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr19:51306624-51308585	GM18951	blood:	n/a	n/a
13	POLR2A	chr19:51305153-51308634	GM12878	blood:	n/a	n/a
14	POLR2A	chr19:51305170-51308571	H1-hESC	embryonic stem cell:	n/a	n/a
15	IRF1	chr19:51306703-51308549	K562	blood:	n/a	chr19:51306800-51306807 chr19:51308224-51308238 chr19:51306932-51306949 chr19:51308347-51308361 chr19:51308280-51308294 chr19:51307441-51307454 chr19:51306937-51306949
16	POLR2A	chr19:51305179-51309471	HepG2	liver:	n/a	n/a
17	POLR2A	chr19:51306458-51308608	K562	blood:	n/a	n/a
18	MYC	chr19:51306752-51307281	MCF10A-Er-Src	breast:	n/a	chr19:51307163-51307172
19	POLR2A	chr19:51305452-51308828	K562	blood:	n/a	n/a
20	POLR2A	chr19:51306040-51308744	MCF10A-Er-Src	breast:	n/a	n/a
21	POLR2A	chr19:51306488-51306833	ECC-1	luminal epithelium:	n/a	n/a
22	WRNIP1	chr19:51306036-51307340	GM12878	blood:	n/a	n/a
23	POLR2A	chr19:51305174-51308584	GM12892	blood:	n/a	n/a
24	POLR2A	chr19:51305338-51308648	GM12891	blood:	n/a	n/a
25	POLR2A	chr19:51306499-51306833	GM12878	blood:	n/a	n/a
26	HCFC1	chr19:51306626-51308827	Hela-S3	cervix:	n/a	n/a
27	POLR2A	chr19:51306050-51308019	K562	blood:	n/a	n/a
28	HEY1	chr19:51305231-51308447	K562	blood:	n/a	chr19:51307531-51307546
29	POLR2A	chr19:51305876-51308037	GM12892	blood:	n/a	n/a
30	POLR2A	chr19:51306175-51308727	IMR90	lung:	n/a	n/a
31	POLR2A	chr19:51306020-51308604	HUVEC	blood vessel:	n/a	n/a
32	POLR2A	chr19:51305307-51308547	Hela-S3	cervix:	n/a	n/a
33	POLR2A	chr19:51306495-51307341	H1-hESC	embryonic stem cell:	n/a	n/a
34	POLR2A	chr19:51306569-51308518	PANC-1	pancreas:	n/a	n/a
35	POLR2A	chr19:51305464-51308657	Hela-S3	cervix:	n/a	n/a
36	POLR2A	chr19:51306006-51306960	U87	brain:	n/a	n/a
37	POLR2A	chr19:51305373-51307998	A549	lung:	n/a	n/a
38	POLR2A	chr19:51306069-51308625	MCF10A-Er-Src	breast:	n/a	n/a
39	MAFF	chr19:51306788-51306832	K562	blood:	n/a	n/a
40	BCL3	chr19:51306784-51308314	A549	lung:	n/a	chr19:51307558-51307571 chr19:51307558-51307567 chr19:51307959-51307968 chr19:51307280-51307289
41	MYC	chr19:51306792-51308545	MCF10A-Er-Src	breast:	n/a	chr19:51308329-51308339 chr19:51308330-51308339 chr19:51308330-51308339 chr19:51308328-51308337 chr19:51308330-51308339 chr19:51307163-51307172 chr19:51308329-51308340
42	MAX	chr19:51306308-51308840	A549	lung:	n/a	chr19:51308329-51308339 chr19:51308330-51308339 chr19:51308330-51308339 chr19:51308328-51308337 chr19:51308330-51308339 chr19:51307163-51307172 chr19:51308329-51308340
43	POLR2A	chr19:51305892-51308632	PFSK-1	brain:	n/a	n/a
44	NFATC1	chr19:51306462-51307058	GM12878	blood:	n/a	n/a
45	MTA3	chr19:51306131-51307387	GM12878	blood:	n/a	n/a
46	POLR2A	chr19:51306750-51308010	ECC-1	luminal epithelium:	n/a	n/a
47	POU2F2	chr19:51306528-51307396	GM12878	blood:	n/a	n/a
48	POLR2A	chr19:51305496-51308422	PFSK-1	brain:	n/a	n/a
49	POLR2A	chr19:51306166-51308579	K562	blood:	n/a	n/a
50	POLR2A	chr19:51305364-51308607	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:51306486..51308352-chr19:51377900..51380168,3	K562	blood:
2	chr19:51225685..51229614-chr19:51306371..51310193,7	MCF-7	breast:
3	chr15:100888968..100891280-chr19:51305902..51308003,2	MCF-7	breast:
4	chr19:51306616..51308250-chr19:51611321..51612835,2	K562	blood:
5	chr19:50878289..50880426-chr19:51306206..51308776,2	K562	blood:
6	chr19:51304876..51308314-chr19:51372660..51375800,4	MCF-7	breast:
7	chr19:51225811..51229710-chr19:51304326..51309315,7	K562	blood:
8	chr19:51305915..51308029-chr19:51455480..51457752,2	K562	blood:
9	chr19:51306023..51307815-chr19:51411885..51414130,3	K562	blood:
10	chr19:51291032..51294383-chr19:51305809..51308243,6	MCF-7	breast:
11	chr19:51221053..51222783-chr19:51305600..51307865,2	K562	blood:
12	chr19:51161291..51162823-chr19:51306692..51308386,2	K562	blood:
13	chr19:51306219..51311443-chr19:51320268..51326410,9	MCF-7	breast:
14	chr14:70233572..70234808-chr19:51306783..51308006,3	Hela-S3	cervix:
15	chr19:51306448..51310717-chr19:51372415..51375235,4	K562	blood:
16	chr19:51306094..51308089-chr20:55841025..55842580,2	MCF-7	breast:
17	chr19:51306173..51309320-chr19:51331029..51336004,5	MCF-7	breast:
18	chr19:51305829..51307927-chr19:51320436..51323745,3	MCF-7	breast:
19	chr19:51306202..51308468-chr19:51372838..51375377,2	K562	blood:
20	chr19:51014538..51017258-chr19:51306499..51308230,2	K562	blood:
21	chr19:50878669..50883054-chr19:51306301..51308717,4	MCF-7	breast:
22	chr19:51305954..51309003-chr19:51339405..51341608,4	K562	blood:
23	chr19:51305909..51308309-chr19:51411302..51414101,3	MCF-7	breast:

Variant related genes	Relation type
SNORD88A	TF binding region
SNORD88C	TF binding region
SNORD88B	TF binding region
C19orf48	TF binding region
ENSG00000189419	Chromatin interaction
ENSG00000226308	Chromatin interaction
ENSG00000167751	Chromatin interaction
ENSG00000167748	Chromatin interaction
ENSG00000174562	Chromatin interaction
ENSG00000161681	Chromatin interaction
ENSG00000101144	Chromatin interaction
ENSG00000142513	Chromatin interaction
ENSG00000100650	Chromatin interaction
ENSG00000167754	Chromatin interaction
ENSG00000167749	Chromatin interaction
ENSG00000235034	Chromatin interaction
ENSG00000204653	Chromatin interaction
ENSG00000161677	Chromatin interaction
ENSG00000267880	Chromatin interaction
ENSG00000131408	Chromatin interaction
ENSG00000105472	Chromatin interaction
ENSG00000142544	Chromatin interaction
ENSG00000267968	Chromatin interaction
ENSG00000180279	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs2247289	0.90[AFR][1000 genomes]
rs2434449	0.89[AFR][1000 genomes]
rs2659059	0.90[AFR][1000 genomes]
rs788887	0.87[AFR][1000 genomes]
rs788889	0.81[AFR][1000 genomes]
rs788890	0.81[AFR][1000 genomes]
rs788891	0.81[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1060760	chr19:50883425-51463712	ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
2	nsv1058177	chr19:50984774-51463712	Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
3	nsv912288	chr19:51283791-51334355	Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	60 gene(s)	inside rSNPs	diseases
4	nsv912289	chr19:51283791-51335943	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	60 gene(s)	inside rSNPs	diseases
5	nsv912290	chr19:51283791-51344483	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	60 gene(s)	inside rSNPs	diseases
6	nsv526232	chr19:51301230-51335943	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	45 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	chr19:51298200-51306800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:51300000-51306800	Weak transcription	Right Atrium	heart
3	chr19:51302000-51307200	Weak transcription	Aorta	Aorta
4	chr19:51302800-51307000	Transcr. at gene 5' and 3'	Hela-S3	cervix
5	chr19:51305200-51307000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr19:51305200-51307400	Transcr. at gene 5' and 3'	Dnd41	blood
7	chr19:51305400-51306800	Transcr. at gene 5' and 3'	HepG2	liver
8	chr19:51305400-51307000	Enhancers	Placenta Amnion	Placenta Amnion
9	chr19:51305400-51307000	Transcr. at gene 5' and 3'	K562	blood
10	chr19:51305400-51307200	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
11	chr19:51305400-51307200	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
12	chr19:51305400-51307200	Transcr. at gene 5' and 3'	A549	lung
13	chr19:51305400-51307200	Transcr. at gene 5' and 3'	NHEK	skin
14	chr19:51305600-51306800	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr19:51305600-51306800	Enhancers	Fetal Brain Male	brain
16	chr19:51305600-51306800	Enhancers	Pancreas	Pancrea
17	chr19:51305600-51307000	Transcr. at gene 5' and 3'	ES-UCSF4 Cell Line	embryonic stem cell
18	chr19:51305600-51307200	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
19	chr19:51305600-51307200	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
20	chr19:51305800-51306800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr19:51305800-51306800	Enhancers	Lung	lung
22	chr19:51305800-51307000	Transcr. at gene 5' and 3'	ES-I3 Cell Line	embryonic stem cell
23	chr19:51305800-51307200	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr19:51305800-51307200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr19:51305800-51307400	Enhancers	Spleen	Spleen
26	chr19:51305800-51309000	Active TSS	HUES64 Cell Line	embryonic stem cell
27	chr19:51306000-51306800	Enhancers	Primary neutrophils fromperipheralblood	blood
28	chr19:51306000-51306800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr19:51306000-51306800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
30	chr19:51306000-51306800	Enhancers	Brain Anterior Caudate	brain
31	chr19:51306000-51306800	Enhancers	Brain Cingulate Gyrus	brain
32	chr19:51306000-51306800	Transcr. at gene 5' and 3'	HMEC	breast
33	chr19:51306000-51307000	Enhancers	Primary monocytes fromperipheralblood	blood
34	chr19:51306000-51307000	Enhancers	Primary B cells from peripheral blood	blood
35	chr19:51306000-51307000	Enhancers	Left Ventricle	heart
36	chr19:51306000-51307000	Enhancers	Stomach Mucosa	stomach
37	chr19:51306000-51307200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr19:51306000-51307200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr19:51306000-51307200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
40	chr19:51306000-51307200	Flanking Active TSS	Brain Germinal Matrix	brain
41	chr19:51306000-51307200	Flanking Active TSS	HSMM	muscle
42	chr19:51306000-51307200	Flanking Active TSS	HUVEC	blood vessel
43	chr19:51306000-51307200	Flanking Active TSS	Osteobl	bone
44	chr19:51306000-51307400	Flanking Active TSS	Primary hematopoietic stem cells	blood
45	chr19:51306000-51307400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr19:51306000-51307400	Flanking Active TSS	Fetal Brain Female	brain
47	chr19:51306000-51307400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
48	chr19:51306000-51307400	Flanking Active TSS	HSMMtube	muscle
49	chr19:51306000-51308600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr19:51306000-51308600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links