Variant report

Variant	rs2074852
Chromosome Location	chr19:39880011-39880012
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	chr19:39875493-39880799	SK-N-MC	brain:	n/a	n/a
2	POLR2A	chr19:39879250-39880035	U87	brain:	n/a	n/a
3	BCL3	chr19:39879962-39882537	A549	lung:	n/a	n/a
4	POLR2A	chr19:39850716-39886400	PANC-1	pancreas:	n/a	n/a
5	POLR2A	chr19:39879003-39880495	U87	brain:	n/a	n/a
6	POLR2A	chr19:39879380-39880471	HUVEC	blood vessel:	n/a	n/a
7	REST	chr19:39879869-39882476	PANC-1	pancreas:	n/a	chr19:39881693-39881703 chr19:39881691-39881711 chr19:39881615-39881625 chr19:39881691-39881705 chr19:39880192-39880205 chr19:39881520-39881533
8	POLR2A	chr19:39879969-39880011	MCF-7	breast:	n/a	n/a
9	POLR2A	chr19:39879929-39880151	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr19:39879909-39880218	HCT-116	colon:	n/a	n/a
11	POLR2A	chr19:39876429-39882671	HepG2	liver:	n/a	n/a
12	POLR2A	chr19:39879250-39880065	U87	brain:	n/a	n/a
13	POLR2A	chr19:39879881-39880473	HL-60	blood:	n/a	n/a
14	POLR2A	chr19:39878769-39880629	K562	blood:	n/a	n/a
15	POLR2A	chr19:39879908-39881021	K562	blood:	n/a	n/a
16	BCL3	chr19:39878998-39880342	A549	lung:	n/a	chr19:39879688-39879701
17	SIN3AK20	chr19:39870428-39883708	PANC-1	pancreas:	n/a	n/a
18	POLR2A	chr19:39878822-39880048	SK-N-SH	brain:	n/a	n/a
19	POLR2A	chr19:39879945-39880944	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr19:39879603-39880040	HCT-116	colon:	n/a	n/a
21	POLR2A	chr19:39878610-39880530	PFSK-1	brain:	n/a	n/a
22	TCF12	chr19:39879881-39882636	A549	lung:	n/a	chr19:39880201-39880211
23	POLR2A	chr19:39879009-39880489	U87	brain:	n/a	n/a
24	POLR2A	chr19:39875542-39882243	K562	blood:	n/a	n/a
25	POLR2A	chr19:39878621-39882617	H1-hESC	embryonic stem cell:	n/a	n/a
26	POLR2A	chr19:39879961-39882312	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:39860348..39862519-chr19:39879962..39882388,3	K562	blood:
2	chr19:39859941..39863633-chr19:39878903..39882994,5	MCF-7	breast:

Variant related genes	Relation type
MED29	TF binding region
PAF1	TF binding region
ENSG00000179134	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1375910	0.81[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs16973342	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16973348	1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs16973350	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16973363	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs16973374	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2067102	1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs251906	0.83[JPT][hapmap]
rs30453	0.91[JPT][hapmap]
rs30454	0.91[JPT][hapmap]
rs30455	0.91[JPT][hapmap]
rs30457	0.91[JPT][hapmap]
rs36264	0.91[JPT][hapmap]
rs36270	0.83[JPT][hapmap]
rs3786949	1.00[JPT][hapmap]
rs3826938	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3865515	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40353	0.83[JPT][hapmap]
rs40441	0.91[JPT][hapmap]
rs562638	0.91[JPT][hapmap]
rs56867744	0.94[ASN][1000 genomes]
rs57411196	1.00[ASN][1000 genomes]
rs57479776	0.81[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs57920235	0.97[ASN][1000 genomes]
rs58586829	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59446951	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62119691	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs62119694	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs62119701	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs62119703	0.81[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs6508860	0.91[JPT][hapmap]
rs685125	0.83[JPT][hapmap]
rs73546049	0.82[EUR][1000 genomes]
rs73546081	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73547916	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs917319	0.91[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911679	chr19:39735106-39924129	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	198 gene(s)	inside rSNPs	diseases
2	nsv1058514	chr19:39744112-39902580	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
3	nsv911680	chr19:39792460-39924129	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	194 gene(s)	inside rSNPs	diseases
4	esv10629	chr19:39811570-39886212	Flanking Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv870133	chr19:39822160-39938468	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers 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 miRNA target site	233 gene(s)	inside rSNPs	diseases
6	nsv911682	chr19:39847132-39914748	Strong transcription Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	179 gene(s)	inside rSNPs	diseases
7	nsv911683	chr19:39847132-39924129	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	185 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39835800-39880200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr19:39835800-39880200	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr19:39836200-39880400	Strong transcription	Primary T cells from cord blood	blood
4	chr19:39836600-39880400	Strong transcription	Primary monocytes fromperipheralblood	blood
5	chr19:39836600-39880400	Strong transcription	Fetal Brain Female	brain
6	chr19:39838600-39880400	Strong transcription	HUES6 Cell Line	embryonic stem cell
7	chr19:39838800-39880200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr19:39842200-39880200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr19:39842200-39880400	Strong transcription	Primary neutrophils fromperipheralblood	blood
10	chr19:39842400-39880400	Strong transcription	Thymus	Thymus
11	chr19:39842600-39880400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr19:39850400-39881000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr19:39852800-39880400	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr19:39856600-39880200	Strong transcription	Fetal Thymus	thymus
15	chr19:39857200-39880200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr19:39857200-39880400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr19:39859000-39880200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr19:39860000-39880400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr19:39864000-39880200	Strong transcription	Placenta	Placenta
20	chr19:39864000-39880400	Strong transcription	Fetal Intestine Small	intestine
21	chr19:39864200-39880400	Strong transcription	Fetal Muscle Leg	muscle
22	chr19:39864400-39880200	Strong transcription	Brain Substantia Nigra	brain
23	chr19:39864400-39880200	Strong transcription	Duodenum Mucosa	Duodenum
24	chr19:39864400-39880200	Strong transcription	Fetal Stomach	stomach
25	chr19:39864400-39880400	Strong transcription	Lung	lung
26	chr19:39864400-39880400	Weak transcription	Right Atrium	heart
27	chr19:39864600-39880400	Strong transcription	Fetal Muscle Trunk	muscle
28	chr19:39864800-39880200	Strong transcription	Brain Inferior Temporal Lobe	brain
29	chr19:39864800-39880400	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chr19:39865000-39880200	Strong transcription	Placenta Amnion	Placenta Amnion
31	chr19:39865000-39880600	Strong transcription	Rectal Mucosa Donor 29	rectum
32	chr19:39865200-39880400	Strong transcription	Colon Smooth Muscle	Colon
33	chr19:39865200-39880400	Strong transcription	NHLF	lung
34	chr19:39865400-39880200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr19:39865600-39880200	Strong transcription	Primary T cells fromperipheralblood	blood
36	chr19:39865600-39880200	Strong transcription	Primary T helper cells PMA-I stimulated	--
37	chr19:39865600-39880200	Strong transcription	Adipose Nuclei	Adipose
38	chr19:39865600-39880200	Strong transcription	Brain Anterior Caudate	brain
39	chr19:39865600-39880200	Strong transcription	Colonic Mucosa	Colon
40	chr19:39865600-39880200	Strong transcription	Ovary	ovary
41	chr19:39865600-39880400	Strong transcription	Muscle Satellite Cultured Cells	--
42	chr19:39865600-39880600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr19:39865800-39880200	Strong transcription	Cortex derived primary cultured neurospheres	brain
44	chr19:39865800-39880200	Strong transcription	Duodenum Smooth Muscle	Duodenum
45	chr19:39865800-39880400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr19:39865800-39880400	Strong transcription	Sigmoid Colon	Sigmoid Colon
47	chr19:39866200-39880200	Strong transcription	Right Ventricle	heart
48	chr19:39866200-39880600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr19:39870000-39880400	Strong transcription	Liver	Liver
50	chr19:39871000-39880400	Strong transcription	Brain Cingulate Gyrus	brain

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