Variant report

Variant	rs10423589
Chromosome Location	chr19:55915262-55915263
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:55915261-55916289	GM12878	blood:	n/a	n/a
2	POLR2A	chr19:55915128-55916611	SK-N-MC	brain:	n/a	n/a
3	POLR2A	chr19:55915250-55916439	K562	blood:	n/a	n/a
4	POLR2A	chr19:55910140-55916359	PFSK-1	brain:	n/a	n/a
5	POLR2A	chr19:55915239-55915791	PANC-1	pancreas:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:55790204..55793295-chr19:55914436..55917425,4	K562	blood:
2	chr19:55766579..55768954-chr19:55914081..55916884,2	K562	blood:
3	chr19:55790480..55793295-chr19:55915028..55917425,3	K562	blood:
4	chr19:55913931..55915922-chr19:55972282..55974856,2	MCF-7	breast:
5	chr19:55865344..55867006-chr19:55913692..55915275,2	MCF-7	breast:
6	chr19:55911623..55913706-chr19:55914461..55917038,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000267093	TF binding region
ENSG00000105063	Chromatin interaction
ENSG00000133265	Chromatin interaction
ENSG00000267093	Chromatin interaction
ENSG00000063241	Chromatin interaction
ENSG00000160471	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10403564	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10403989	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10404049	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10404370	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10405802	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10407066	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10408088	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10408448	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10408525	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10408540	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10410269	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10411984	0.81[AFR][1000 genomes]
rs10415365	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10416908	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10420818	0.93[AFR][1000 genomes]
rs10421889	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10424289	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10424652	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10425107	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10425362	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10425596	0.82[AFR][1000 genomes]
rs28408730	0.93[AFR][1000 genomes]
rs28536711	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28540780	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28797308	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59698058	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61468173	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73617871	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73617888	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73617896	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73619606	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73619611	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73619651	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065760	chr19:55721521-55929740	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	212 gene(s)	inside rSNPs	diseases
2	nsv912456	chr19:55725410-55925500	Weak transcription Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	212 gene(s)	inside rSNPs	diseases
3	nsv912457	chr19:55725410-56019597	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	228 gene(s)	inside rSNPs	diseases
4	nsv432086	chr19:55807586-56050844	Weak transcription Bivalent Enhancer Genic enhancers Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	220 gene(s)	inside rSNPs	diseases
5	nsv912462	chr19:55845386-55925500	Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	203 gene(s)	inside rSNPs	diseases
6	nsv912463	chr19:55845386-56004901	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases
7	nsv912464	chr19:55850269-55921164	Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	203 gene(s)	inside rSNPs	diseases
8	nsv912465	chr19:55854313-55935184	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh 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	196 gene(s)	inside rSNPs	diseases
9	nsv912473	chr19:55874642-56145428	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer 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	233 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	chr19:55900200-55918400	Weak transcription	Psoas Muscle	Psoas
2	chr19:55900600-55917600	Weak transcription	Stomach Mucosa	stomach
3	chr19:55901000-55917800	Weak transcription	Right Atrium	heart
4	chr19:55901800-55916800	Weak transcription	Fetal Brain Male	brain
5	chr19:55902200-55917400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr19:55910200-55917000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr19:55910800-55917200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr19:55910800-55917600	Strong transcription	Brain Anterior Caudate	brain
9	chr19:55911000-55915400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr19:55911000-55915800	Strong transcription	Cortex derived primary cultured neurospheres	brain
11	chr19:55911000-55917000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr19:55911000-55917000	Strong transcription	Primary B cells from peripheral blood	blood
13	chr19:55911000-55917000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr19:55911000-55917000	Strong transcription	Fetal Intestine Large	intestine
15	chr19:55911000-55917000	Strong transcription	Stomach Smooth Muscle	stomach
16	chr19:55911200-55915400	Strong transcription	Fetal Thymus	thymus
17	chr19:55911200-55915800	Strong transcription	Primary T cells from cord blood	blood
18	chr19:55911200-55916800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr19:55911200-55917000	Strong transcription	Fetal Stomach	stomach
20	chr19:55911200-55917200	Strong transcription	Brain Hippocampus Middle	brain
21	chr19:55911400-55915400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr19:55911400-55916000	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr19:55911400-55916800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr19:55911400-55917000	Strong transcription	Duodenum Mucosa	Duodenum
25	chr19:55911600-55915400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr19:55911600-55915400	Genic enhancers	A549	lung
27	chr19:55911600-55916000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr19:55911600-55916200	Strong transcription	Placenta Amnion	Placenta Amnion
29	chr19:55911600-55916600	Strong transcription	Primary T helper cells PMA-I stimulated	--
30	chr19:55911600-55916600	Strong transcription	NH-A	brain
31	chr19:55911600-55916800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr19:55911600-55916800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr19:55911600-55917000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
34	chr19:55911600-55917000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
35	chr19:55911600-55917000	Strong transcription	Primary T helper cells fromperipheralblood	blood
36	chr19:55911800-55915400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr19:55911800-55915400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr19:55911800-55915400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr19:55911800-55915400	Strong transcription	Spleen	Spleen
40	chr19:55911800-55915600	Strong transcription	H1 Cell Line	embryonic stem cell
41	chr19:55911800-55915600	Strong transcription	NHLF	lung
42	chr19:55911800-55915800	Strong transcription	Primary hematopoietic stem cells	blood
43	chr19:55911800-55916000	Strong transcription	Primary T cells fromperipheralblood	blood
44	chr19:55911800-55916000	Strong transcription	Liver	Liver
45	chr19:55911800-55916200	Strong transcription	Primary neutrophils fromperipheralblood	blood
46	chr19:55911800-55916200	Strong transcription	Ovary	ovary
47	chr19:55911800-55916200	Strong transcription	Rectal Mucosa Donor 31	rectum
48	chr19:55911800-55916200	Strong transcription	Rectal Smooth Muscle	rectum
49	chr19:55911800-55916400	Strong transcription	Primary T killer memory cells from peripheral blood	blood
50	chr19:55911800-55916400	Strong transcription	Brain Cingulate Gyrus	brain

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