Variant report

Variant	rs28625363
Chromosome Location	chr19:35755706-35755707
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:79)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:79 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:35755153-35756095	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr19:35754617-35758779	ECC-1	luminal epithelium:	n/a	n/a
3	POLR2A	chr19:35754986-35756728	U87	brain:	n/a	n/a
4	POLR2A	chr19:35754823-35759078	PBDE	blood:	n/a	n/a
5	PBX3	chr19:35755123-35755834	A549	lung:	n/a	chr19:35755806-35755815
6	POLR2A	chr19:35754928-35760887	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr19:35754084-35759312	PANC-1	pancreas:	n/a	n/a
8	POLR2A	chr19:35755260-35755940	HUVEC	blood vessel:	n/a	n/a
9	POLR2A	chr19:35754965-35760872	K562	blood:	n/a	n/a
10	POLR2A	chr19:35754925-35756051	GM12892	blood:	n/a	n/a
11	POLR2A	chr19:35755196-35755956	A549	lung:	n/a	n/a
12	POLR2A	chr19:35755235-35756842	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr19:35755278-35755908	A549	lung:	n/a	n/a
14	POLR2A	chr19:35754917-35759308	HepG2	liver:	n/a	n/a
15	POLR2A	chr19:35751612-35760840	K562	blood:	n/a	n/a
16	POLR2A	chr19:35754833-35756779	HL-60	blood:	n/a	n/a
17	POLR2A	chr19:35751524-35759415	MCF-7	breast:	n/a	n/a
18	POLR2A	chr19:35754928-35759882	K562	blood:	n/a	n/a
19	POLR2A	chr19:35754868-35757342	PFSK-1	brain:	n/a	n/a
20	POLR2A	chr19:35754937-35759358	K562	blood:	n/a	n/a
21	POLR2A	chr19:35755421-35757718	HepG2	liver:	n/a	n/a
22	POLR2A	chr19:35754929-35759928	GM12878	blood:	n/a	n/a
23	POLR2A	chr19:35755074-35756544	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr19:35755314-35755820	GM12892	blood:	n/a	n/a
25	POLR2A	chr19:35754913-35759311	GM12891	blood:	n/a	n/a
26	POLR2A	chr19:35755244-35757351	Hela-S3	cervix:	n/a	n/a
27	POLR2A	chr19:35755269-35756041	U87	brain:	n/a	n/a
28	POLR2A	chr19:35755214-35756353	GM12891	blood:	n/a	n/a
29	POLR2A	chr19:35754961-35760825	GM18505	blood:	n/a	n/a
30	POLR2A	chr19:35755048-35759310	HepG2	liver:	n/a	n/a
31	POLR2A	chr19:35755512-35755748	H1-hESC	embryonic stem cell:	n/a	n/a
32	POLR2A	chr19:35754910-35759941	K562	blood:	n/a	n/a
33	POLR2A	chr19:35754929-35756517	HL-60	blood:	n/a	n/a
34	TCF12	chr19:35754750-35759258	A549	lung:	n/a	chr19:35757445-35757455 chr19:35759218-35759228
35	POLR2A	chr19:35755293-35755744	MCF-7	breast:	n/a	n/a
36	POLR2A	chr19:35754894-35755866	HepG2	liver:	n/a	n/a
37	BCL3	chr19:35754891-35756504	A549	lung:	n/a	n/a
38	POLR2A	chr19:35755202-35759271	HepG2	liver:	n/a	n/a
39	MTA3	chr19:35754915-35755770	GM12878	blood:	n/a	n/a
40	POLR2A	chr19:35752075-35759311	HepG2	liver:	n/a	n/a
41	POLR2A	chr19:35754928-35756734	HCT-116	colon:	n/a	n/a
42	POLR2A	chr19:35754935-35756651	A549	lung:	n/a	n/a
43	POLR2A	chr19:35755282-35755923	A549	lung:	n/a	n/a
44	POLR2A	chr19:35751472-35759661	MCF10A-Er-Src	breast:	n/a	n/a
45	POLR2A	chr19:35754935-35759965	Hela-S3	cervix:	n/a	n/a
46	POLR2A	chr19:35754789-35759375	PANC-1	pancreas:	n/a	n/a
47	POLR2A	chr19:35754952-35759682	Hela-S3	cervix:	n/a	n/a
48	POLR2A	chr19:35754911-35759658	HCT-116	colon:	n/a	n/a
49	POLR2A	chr19:35755618-35755868	SK-N-SH	brain:	n/a	n/a
50	POLR2A	chr19:35755691-35755923	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:35653961..35659020-chr19:35755691..35760689,8	K562	blood:
2	chr19:35752101..35756218-chr19:36205472..36209304,3	MCF-7	breast:
3	chr19:35637271..35639963-chr19:35753955..35756659,2	K562	blood:
4	chr19:35631425..35638367-chr19:35753629..35761294,12	MCF-7	breast:
5	chr19:35755149..35764508-chr19:35799437..35813142,44	MCF-7	breast:
6	chr19:35631758..35633749-chr19:35755549..35757445,2	K562	blood:
7	chr19:35753841..35756119-chr19:35797821..35799359,2	MCF-7	breast:
8	chr19:35755034..35756836-chr19:35817382..35820028,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-USF2-2	chr19:35754945-35755707	ENSG00000268947.1

No data

Variant related genes	Relation type
USF2	TF binding region
LSR	TF binding region
ENSG00000272333	Chromatin interaction
ENSG00000221946	Chromatin interaction
ENSG00000266964	Chromatin interaction
ENSG00000153902	Chromatin interaction
ENSG00000105695	Chromatin interaction
ENSG00000012124	Chromatin interaction
ENSG00000089327	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10402152	1.00[AMR][1000 genomes]
rs10403374	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10408815	0.83[AFR][1000 genomes]
rs10410327	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10414019	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10416084	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10416544	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10416795	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10419861	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10423421	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10425979	1.00[AMR][1000 genomes]
rs10426676	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28592719	0.83[AFR][1000 genomes]
rs28626713	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28673075	0.83[AFR][1000 genomes]
rs60886964	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432045	chr19:35556260-36520760	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv1060100	chr19:35658505-36170042	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv543993	chr19:35658505-36170042	Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
4	nsv510765	chr19:35708226-35890668	Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
5	esv2758497	chr19:35711078-35887113	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
6	esv2758758	chr19:35711078-35887113	Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
7	nsv911618	chr19:35734107-35807845	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
8	esv1836312	chr19:35741456-35786868	Enhancers Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	n/a
9	nsv911619	chr19:35749563-35775441	Weak transcription Genic enhancers Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	n/a
10	nsv911620	chr19:35752917-35771382	Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	n/a
11	nsv911621	chr19:35752917-35772471	Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	n/a
12	nsv911622	chr19:35752917-35773146	Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	n/a
13	nsv911623	chr19:35752917-35775441	Flanking Active TSS Genic enhancers Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:35741200-35758000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr19:35741400-35757800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr19:35742000-35756200	Strong transcription	NHEK	skin
4	chr19:35743800-35756600	Strong transcription	Rectal Mucosa Donor 29	rectum
5	chr19:35744400-35757600	Strong transcription	Fetal Intestine Large	intestine
6	chr19:35744800-35757600	Strong transcription	H1 Cell Line	embryonic stem cell
7	chr19:35744800-35757600	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr19:35744800-35757800	Strong transcription	H9 Cell Line	embryonic stem cell
9	chr19:35744800-35758000	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr19:35745000-35757800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr19:35746600-35757600	Strong transcription	Fetal Intestine Small	intestine
12	chr19:35746600-35757600	Weak transcription	Hela-S3	cervix
13	chr19:35746800-35756000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr19:35748400-35756000	Strong transcription	Duodenum Mucosa	Duodenum
15	chr19:35748800-35756600	Weak transcription	Primary T cells from cord blood	blood
16	chr19:35748800-35757600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr19:35749000-35756000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr19:35749000-35756200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr19:35749000-35756600	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr19:35749000-35757000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr19:35749000-35758000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr19:35749200-35756200	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr19:35749200-35756600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr19:35749400-35757600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
25	chr19:35750600-35755800	Strong transcription	Rectal Mucosa Donor 31	rectum
26	chr19:35752000-35756400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr19:35752400-35756400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr19:35752600-35755800	Enhancers	Placenta	Placenta
29	chr19:35752600-35758000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr19:35753200-35756000	Strong transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr19:35753200-35756400	Weak transcription	Right Atrium	heart
32	chr19:35753200-35757400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr19:35753400-35755800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr19:35753600-35756000	Weak transcription	Left Ventricle	heart
35	chr19:35753800-35756000	Weak transcription	Stomach Smooth Muscle	stomach
36	chr19:35753800-35756200	Weak transcription	Lung	lung
37	chr19:35753800-35756200	Weak transcription	Psoas Muscle	Psoas
38	chr19:35753800-35756200	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr19:35753800-35756600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr19:35753800-35757000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr19:35753800-35757600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr19:35754200-35757400	Weak transcription	Fetal Brain Male	brain
43	chr19:35754400-35755800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr19:35754400-35756200	Enhancers	Primary B cells from peripheral blood	blood
45	chr19:35754600-35756800	Weak transcription	A549	lung
46	chr19:35754600-35757000	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr19:35754600-35757400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr19:35754800-35756000	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr19:35754800-35756200	Genic enhancers	Pancreas	Pancrea
50	chr19:35754800-35756800	Weak transcription	Brain Germinal Matrix	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links