Variant report

Variant	rs2659063
Chromosome Location	chr19:51306302-51306303
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:51)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:51 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:51305171-51308575	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr19:51305218-51308754	SK-N-MC	brain:	n/a	n/a
3	POLR2A	chr19:51306295-51306466	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr19:51305213-51308097	GM12892	blood:	n/a	n/a
5	POLR2A	chr19:51305850-51308510	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr19:51305153-51308634	GM12878	blood:	n/a	n/a
7	POLR2A	chr19:51305170-51308571	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr19:51305179-51309471	HepG2	liver:	n/a	n/a
9	POLR2A	chr19:51305452-51308828	K562	blood:	n/a	n/a
10	POLR2A	chr19:51306040-51308744	MCF10A-Er-Src	breast:	n/a	n/a
11	WRNIP1	chr19:51306036-51307340	GM12878	blood:	n/a	n/a
12	POLR2A	chr19:51305174-51308584	GM12892	blood:	n/a	n/a
13	POLR2A	chr19:51305338-51308648	GM12891	blood:	n/a	n/a
14	POLR2A	chr19:51306050-51308019	K562	blood:	n/a	n/a
15	HEY1	chr19:51305231-51308447	K562	blood:	n/a	chr19:51307531-51307546
16	POLR2A	chr19:51305876-51308037	GM12892	blood:	n/a	n/a
17	POLR2A	chr19:51306175-51308727	IMR90	lung:	n/a	n/a
18	POLR2A	chr19:51306020-51308604	HUVEC	blood vessel:	n/a	n/a
19	POLR2A	chr19:51305307-51308547	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr19:51306015-51306507	PANC-1	pancreas:	n/a	n/a
21	HEY1	chr19:51306238-51306586	HepG2	liver:	n/a	n/a
22	POLR2A	chr19:51305464-51308657	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr19:51306006-51306960	U87	brain:	n/a	n/a
24	POLR2A	chr19:51305373-51307998	A549	lung:	n/a	n/a
25	POLR2A	chr19:51306069-51308625	MCF10A-Er-Src	breast:	n/a	n/a
26	POLR2A	chr19:51305892-51308632	PFSK-1	brain:	n/a	n/a
27	MTA3	chr19:51306131-51307387	GM12878	blood:	n/a	n/a
28	POLR2A	chr19:51305496-51308422	PFSK-1	brain:	n/a	n/a
29	POLR2A	chr19:51306166-51308579	K562	blood:	n/a	n/a
30	POLR2A	chr19:51305364-51308607	GM12878	blood:	n/a	n/a
31	POLR2A	chr19:51305876-51308258	H1-hESC	embryonic stem cell:	n/a	n/a
32	POLR2A	chr19:51306060-51308589	K562	blood:	n/a	n/a
33	HEY1	chr19:51306283-51306511	K562	blood:	n/a	n/a
34	POLR2A	chr19:51305176-51308591	GM12878	blood:	n/a	n/a
35	POLR2A	chr19:51306036-51308575	HepG2	liver:	n/a	n/a
36	POLR2A	chr19:51305396-51308628	GM19099	blood:	n/a	n/a
37	POLR2A	chr19:51305263-51307426	GM12891	blood:	n/a	n/a
38	POLR2A	chr19:51305034-51308640	GM12892	blood:	n/a	n/a
39	POLR2A	chr19:51305966-51308626	HL-60	blood:	n/a	n/a
40	POLR2A	chr19:51305200-51308131	GM12891	blood:	n/a	n/a
41	POLR2A	chr19:51305309-51308551	H1-hESC	embryonic stem cell:	n/a	n/a
42	POLR2A	chr19:51306243-51307342	GM12891	blood:	n/a	n/a
43	POLR2A	chr19:51305326-51308592	K562	blood:	n/a	n/a
44	POLR2A	chr19:51305343-51308586	K562	blood:	n/a	n/a
45	POLR2A	chr19:51305272-51308541	K562	blood:	n/a	n/a
46	POLR2A	chr19:51305761-51308074	GM12891	blood:	n/a	n/a
47	CHD1	chr19:51306232-51308100	H1-hESC	embryonic stem cell:	n/a	chr19:51307601-51307611
48	POLR2A	chr19:51306003-51306374	HCT-116	colon:	n/a	n/a
49	USF2	chr19:51306156-51308633	Hela-S3	cervix:	n/a	chr19:51308328-51308339 chr19:51307745-51307761
50	POLR2A	chr19:51306176-51306638	ECC-1	luminal epithelium:	n/a	n/a

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:100888968..100891280-chr19:51305902..51308003,2	MCF-7	breast:
2	chr19:50878289..50880426-chr19:51306206..51308776,2	K562	blood:
3	chr19:51304876..51308314-chr19:51372660..51375800,4	MCF-7	breast:
4	chr19:51225811..51229710-chr19:51304326..51309315,7	K562	blood:
5	chr19:51305915..51308029-chr19:51455480..51457752,2	K562	blood:
6	chr19:51306023..51307815-chr19:51411885..51414130,3	K562	blood:
7	chr19:51291032..51294383-chr19:51305809..51308243,6	MCF-7	breast:
8	chr19:51221053..51222783-chr19:51305600..51307865,2	K562	blood:
9	chr19:51306219..51311443-chr19:51320268..51326410,9	MCF-7	breast:
10	chr19:51306094..51308089-chr20:55841025..55842580,2	MCF-7	breast:
11	chr19:51306173..51309320-chr19:51331029..51336004,5	MCF-7	breast:
12	chr19:51305829..51307927-chr19:51320436..51323745,3	MCF-7	breast:
13	chr19:51306202..51308468-chr19:51372838..51375377,2	K562	blood:
14	chr19:50878669..50883054-chr19:51306301..51308717,4	MCF-7	breast:
15	chr19:51305954..51309003-chr19:51339405..51341608,4	K562	blood:
16	chr19:51305909..51308309-chr19:51411302..51414101,3	MCF-7	breast:

No data

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

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10412862	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10412900	1.00[JPT][hapmap];0.91[YRI][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12978675	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12979334	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12979351	1.00[CEU][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17800375	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2162784	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2247216	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap]
rs2560932	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2659060	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2659064	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs266112	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs266121	0.84[CHB][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs266124	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212855	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap]
rs36046465	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3810283	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3810284	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57028658	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57906560	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58596241	0.88[ASN][1000 genomes]
rs59925776	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60175380	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60471273	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60817149	0.85[ASN][1000 genomes]
rs67085056	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67367861	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73584988	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73584997	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73585002	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73587469	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73587471	0.89[EUR][1000 genomes];0.92[ASN][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	chr19:51302200-51306600	Weak transcription	Colon Smooth Muscle	Colon
5	chr19:51302200-51306600	Weak transcription	Small Intestine	intestine
6	chr19:51302800-51307000	Transcr. at gene 5' and 3'	Hela-S3	cervix
7	chr19:51305000-51306400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr19:51305200-51306600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr19:51305200-51307000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr19:51305200-51307400	Transcr. at gene 5' and 3'	Dnd41	blood
11	chr19:51305400-51306400	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr19:51305400-51306400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr19:51305400-51306400	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
14	chr19:51305400-51306600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr19:51305400-51306800	Transcr. at gene 5' and 3'	HepG2	liver
16	chr19:51305400-51307000	Enhancers	Placenta Amnion	Placenta Amnion
17	chr19:51305400-51307000	Transcr. at gene 5' and 3'	K562	blood
18	chr19:51305400-51307200	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
19	chr19:51305400-51307200	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
20	chr19:51305400-51307200	Transcr. at gene 5' and 3'	A549	lung
21	chr19:51305400-51307200	Transcr. at gene 5' and 3'	NHEK	skin
22	chr19:51305600-51306400	Genic enhancers	Fetal Muscle Trunk	muscle
23	chr19:51305600-51306600	Enhancers	Primary T cells fromperipheralblood	blood
24	chr19:51305600-51306600	Enhancers	Gastric	stomach
25	chr19:51305600-51306600	Enhancers	Rectal Mucosa Donor 31	rectum
26	chr19:51305600-51306800	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr19:51305600-51306800	Enhancers	Fetal Brain Male	brain
28	chr19:51305600-51306800	Enhancers	Pancreas	Pancrea
29	chr19:51305600-51307000	Transcr. at gene 5' and 3'	ES-UCSF4 Cell Line	embryonic stem cell
30	chr19:51305600-51307200	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
31	chr19:51305600-51307200	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
32	chr19:51305800-51306400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
33	chr19:51305800-51306400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr19:51305800-51306400	Enhancers	Brain Angular Gyrus	brain
35	chr19:51305800-51306400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
36	chr19:51305800-51306400	Enhancers	Fetal Muscle Leg	muscle
37	chr19:51305800-51306600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
38	chr19:51305800-51306600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
39	chr19:51305800-51306600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr19:51305800-51306600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr19:51305800-51306600	Enhancers	Liver	Liver
42	chr19:51305800-51306800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
43	chr19:51305800-51306800	Enhancers	Lung	lung
44	chr19:51305800-51307000	Transcr. at gene 5' and 3'	ES-I3 Cell Line	embryonic stem cell
45	chr19:51305800-51307200	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr19:51305800-51307200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr19:51305800-51307400	Enhancers	Spleen	Spleen
48	chr19:51305800-51309000	Active TSS	HUES64 Cell Line	embryonic stem cell
49	chr19:51306000-51306400	Flanking Active TSS	H1 Cell Line	embryonic stem cell
50	chr19:51306000-51306400	Flanking Active TSS	H9 Cell Line	embryonic stem cell

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