Variant report

Variant	rs34259399
Chromosome Location	chr19:35757427-35757428
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:77)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:77 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:35756975-35759966	MCF-7	breast:	n/a	n/a
2	POLR2A	chr19:35754617-35758779	ECC-1	luminal epithelium:	n/a	n/a
3	POLR2A	chr19:35756605-35760886	GM19193	blood:	n/a	n/a
4	POLR2A	chr19:35756735-35759378	HCT-116	colon:	n/a	n/a
5	POLR2A	chr19:35754823-35759078	PBDE	blood:	n/a	n/a
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	chr19:35757150-35759016	K562	blood:	n/a	n/a
9	POLR2A	chr19:35754965-35760872	K562	blood:	n/a	n/a
10	POLR2A	chr19:35756919-35757743	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr19:35757036-35760953	GM18951	blood:	n/a	n/a
12	POLR2A	chr19:35754917-35759308	HepG2	liver:	n/a	n/a
13	POLR2A	chr19:35751612-35760840	K562	blood:	n/a	n/a
14	POLR2A	chr19:35751524-35759415	MCF-7	breast:	n/a	n/a
15	POLR2A	chr19:35754928-35759882	K562	blood:	n/a	n/a
16	POLR2A	chr19:35754937-35759358	K562	blood:	n/a	n/a
17	MAX	chr19:35757379-35761135	A549	lung:	n/a	chr19:35760929-35760939 chr19:35757438-35757448
18	POLR2A	chr19:35757151-35757595	ProgFib	skin:	n/a	n/a
19	POLR2A	chr19:35755421-35757718	HepG2	liver:	n/a	n/a
20	POLR2A	chr19:35754929-35759928	GM12878	blood:	n/a	n/a
21	POLR2A	chr19:35755910-35759378	ECC-1	luminal epithelium:	n/a	n/a
22	POLR2A	chr19:35757213-35760885	GM15510	blood:	n/a	n/a
23	POLR2A	chr19:35756947-35758743	HepG2	liver:	n/a	n/a
24	POLR2A	chr19:35757391-35757480	GM12878	blood:	n/a	n/a
25	POLR2A	chr19:35754913-35759311	GM12891	blood:	n/a	n/a
26	POLR2A	chr19:35756936-35758241	HepG2	liver:	n/a	n/a
27	POLR2A	chr19:35756845-35759466	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr19:35754961-35760825	GM18505	blood:	n/a	n/a
29	POLR2A	chr19:35755048-35759310	HepG2	liver:	n/a	n/a
30	POLR2A	chr19:35754910-35759941	K562	blood:	n/a	n/a
31	POLR2A	chr19:35757099-35760697	GM12892	blood:	n/a	n/a
32	POLR2A	chr19:35756933-35757542	U87	brain:	n/a	n/a
33	TCF12	chr19:35754750-35759258	A549	lung:	n/a	chr19:35757445-35757455 chr19:35759218-35759228
34	POLR2A	chr19:35757366-35759374	GM12891	blood:	n/a	n/a
35	POLR2A	chr19:35755202-35759271	HepG2	liver:	n/a	n/a
36	POLR2A	chr19:35756968-35759922	A549	lung:	n/a	n/a
37	POLR2A	chr19:35752075-35759311	HepG2	liver:	n/a	n/a
38	MTA3	chr19:35756764-35759000	GM12878	blood:	n/a	n/a
39	POLR2A	chr19:35751472-35759661	MCF10A-Er-Src	breast:	n/a	n/a
40	POLR2A	chr19:35756944-35758759	A549	lung:	n/a	n/a
41	POLR2A	chr19:35754935-35759965	Hela-S3	cervix:	n/a	n/a
42	POLR2A	chr19:35757088-35760800	GM18526	blood:	n/a	n/a
43	POLR2A	chr19:35757028-35757822	H1-hESC	embryonic stem cell:	n/a	n/a
44	POLR2A	chr19:35754789-35759375	PANC-1	pancreas:	n/a	n/a
45	POLR2A	chr19:35757046-35758754	GM12878	blood:	n/a	n/a
46	HEY1	chr19:35756970-35757430	HepG2	liver:	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	chr19:35757035-35759349	GM12878	blood:	n/a	n/a
50	CHD2	chr19:35757413-35757648	Hela-S3	cervix:	n/a	n/a

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:35653961..35659020-chr19:35755691..35760689,8	K562	blood:
2	chr19:35631425..35638367-chr19:35753629..35761294,12	MCF-7	breast:
3	chr19:35755149..35764508-chr19:35799437..35813142,44	MCF-7	breast:
4	chr19:35489265..35492467-chr19:35757325..35761392,4	MCF-7	breast:
5	chr19:35601805..35607657-chr19:35757139..35762248,8	MCF-7	breast:
6	chr19:35757206..35760502-chr19:36133299..36134978,3	K562	blood:
7	chr19:35653961..35658211-chr19:35756444..35760028,4	K562	blood:
8	chr19:35756917..35760158-chr19:36118192..36121519,3	K562	blood:
9	chr19:35609312..35611565-chr19:35756942..35759045,2	MCF-7	breast:
10	chr19:35756455..35758959-chr19:35940414..35943178,2	MCF-7	breast:
11	chr19:35631758..35633749-chr19:35755549..35757445,2	K562	blood:
12	chr19:35519941..35521623-chr19:35755963..35757596,2	MCF-7	breast:
13	chr19:35757401..35760609-chr19:35817502..35820242,3	MCF-7	breast:
14	chr19:35757352..35763490-chr19:35798817..35804347,10	MCF-7	breast:

No data

Variant related genes	Relation type
USF2	TF binding region
ENSG00000153902	Chromatin interaction
ENSG00000105695	Chromatin interaction
ENSG00000105711	Chromatin interaction
ENSG00000266964	Chromatin interaction
ENSG00000089356	Chromatin interaction
ENSG00000126254	Chromatin interaction
ENSG00000105672	Chromatin interaction
ENSG00000269303	Chromatin interaction
ENSG00000012124	Chromatin interaction
ENSG00000221946	Chromatin interaction
ENSG00000089351	Chromatin interaction
ENSG00000089327	Chromatin interaction
ENSG00000126262	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs16970163	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2291532	0.84[EUR][1000 genomes]
rs482324	0.93[EUR][1000 genomes]
rs542977	0.88[EUR][1000 genomes]
rs55850007	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56116175	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56138958	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs569596	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7248140	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73029957	0.89[ASN][1000 genomes]
rs73029989	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73030000	1.00[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs8100411	0.95[EUR][1000 genomes];0.92[ASN][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:116 , 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	chr19:35744400-35757600	Strong transcription	Fetal Intestine Large	intestine
4	chr19:35744800-35757600	Strong transcription	H1 Cell Line	embryonic stem cell
5	chr19:35744800-35757600	Strong transcription	HUES48 Cell Line	embryonic stem cell
6	chr19:35744800-35757800	Strong transcription	H9 Cell Line	embryonic stem cell
7	chr19:35744800-35758000	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr19:35745000-35757800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
9	chr19:35746600-35757600	Strong transcription	Fetal Intestine Small	intestine
10	chr19:35746600-35757600	Weak transcription	Hela-S3	cervix
11	chr19:35748800-35757600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr19:35749000-35758000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr19:35749400-35757600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
14	chr19:35752600-35758000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr19:35753800-35757600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr19:35754800-35757600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
17	chr19:35754800-35757800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr19:35754800-35758200	Enhancers	Primary B cells from cord blood	blood
19	chr19:35755000-35757600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr19:35755000-35757600	Enhancers	Adipose Nuclei	Adipose
21	chr19:35755000-35757600	Enhancers	Brain Cingulate Gyrus	brain
22	chr19:35755000-35757800	Enhancers	Primary T helper cells fromperipheralblood	blood
23	chr19:35755000-35757800	Enhancers	Monocytes-CD14+_RO01746	blood
24	chr19:35755000-35758200	Enhancers	Primary monocytes fromperipheralblood	blood
25	chr19:35755200-35757600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr19:35755200-35757800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
27	chr19:35755200-35758000	Enhancers	Spleen	Spleen
28	chr19:35755200-35758400	Enhancers	Fetal Heart	heart
29	chr19:35755400-35757600	Genic enhancers	GM12878-XiMat	blood
30	chr19:35755400-35757800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr19:35755400-35757800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr19:35755400-35757800	Enhancers	Fetal Thymus	thymus
33	chr19:35755400-35758000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
34	chr19:35755400-35758000	Genic enhancers	Gastric	stomach
35	chr19:35755600-35757600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr19:35755600-35757600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr19:35755600-35757600	Genic enhancers	Colonic Mucosa	Colon
38	chr19:35755600-35758000	Enhancers	Primary neutrophils fromperipheralblood	blood
39	chr19:35755600-35758000	Weak transcription	Fetal Kidney	kidney
40	chr19:35755800-35757600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr19:35755800-35757600	Weak transcription	Stomach Mucosa	stomach
42	chr19:35755800-35757600	Genic enhancers	HMEC	breast
43	chr19:35755800-35757800	Genic enhancers	Placenta	Placenta
44	chr19:35755800-35757800	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr19:35755800-35758000	Enhancers	NHDF-Ad	bronchial
46	chr19:35756000-35757800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr19:35756000-35757800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr19:35756000-35757800	Enhancers	Left Ventricle	heart
49	chr19:35756000-35758200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr19:35756200-35757800	Enhancers	Primary T helper cells PMA-I stimulated	--

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