Variant report

Variant	rs58962417
Chromosome Location	chr19:53140834-53140835
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	chr19:53140814-53141749	GM12891	blood:	n/a	n/a
2	POLR2A	chr19:53140829-53142173	IMR90	lung:	n/a	n/a
3	POLR2A	chr19:53140111-53142148	GM12892	blood:	n/a	n/a
4	POLR2A	chr19:53140803-53141852	K562	blood:	n/a	n/a
5	POLR2A	chr19:53140759-53141760	K562	blood:	n/a	n/a
6	POLR2A	chr19:53140652-53141971	GM12891	blood:	n/a	n/a
7	POLR2A	chr19:53140135-53142012	GM12878	blood:	n/a	n/a
8	POLR2A	chr19:53140756-53141786	GM12891	blood:	n/a	n/a
9	PAX5	chr19:53140795-53142082	GM12878	blood:	n/a	chr19:53141336-53141345
10	POLR2A	chr19:53140366-53142176	GM12892	blood:	n/a	n/a
11	POLR2A	chr19:53140421-53141697	GM12892	blood:	n/a	n/a
12	POLR2A	chr19:53140827-53141914	GM12878	blood:	n/a	n/a
13	POLR2A	chr19:53140773-53142211	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr19:53139933-53142093	GM12878	blood:	n/a	n/a
15	MXI1	chr19:53140742-53142548	SK-N-SH	brain:	n/a	n/a
16	POLR2A	chr19:53140730-53141816	PANC-1	pancreas:	n/a	n/a
17	MTA3	chr19:53140755-53141779	GM12878	blood:	n/a	n/a
18	HCFC1	chr19:53140827-53141938	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr19:53140714-53141961	GM12878	blood:	n/a	n/a
20	POU2F2	chr19:53140810-53142122	GM12878	blood:	n/a	chr19:53141107-53141119 chr19:53141882-53141895
21	POLR2A	chr19:53140831-53141887	HUVEC	blood vessel:	n/a	n/a
22	POLR2A	chr19:53140826-53141764	GM12878	blood:	n/a	n/a
23	MXI1	chr19:53140800-53142664	IMR90	lung:	n/a	n/a
24	MAZ	chr19:53140640-53142408	IMR90	lung:	n/a	chr19:53141729-53141739 chr19:53141661-53141671
25	POLR2A	chr19:53140397-53142088	GM12892	blood:	n/a	n/a
26	POLR2A	chr19:53140751-53141888	SK-N-MC	brain:	n/a	n/a
27	HEY1	chr19:53140815-53142009	K562	blood:	n/a	chr19:53141371-53141386
28	POLR2A	chr19:53140810-53141784	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:53139623..53144311-chr19:53192220..53194807,4	MCF-7	breast:
2	chr19:53140133..53142689-chr19:53604558..53606639,2	MCF-7	breast:

Variant related genes	Relation type
ZNF83	TF binding region
ENSG00000170949	Chromatin interaction
ENSG00000167766	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11084172	0.98[ASN][1000 genomes]
rs11878250	0.98[ASN][1000 genomes]
rs11878254	0.93[ASN][1000 genomes]
rs11880764	0.98[ASN][1000 genomes]
rs12460641	0.91[ASN][1000 genomes]
rs12460668	0.98[ASN][1000 genomes]
rs12462943	0.91[ASN][1000 genomes]
rs12610290	0.97[ASN][1000 genomes]
rs8106428	0.95[ASN][1000 genomes]
rs8107336	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057296	chr19:52950339-53396986	Weak transcription Active TSS ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv833874	chr19:53058014-53257875	Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv912305	chr19:53092465-53349850	Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv912306	chr19:53092465-53400760	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	nsv912307	chr19:53092465-53433054	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	nsv912308	chr19:53092465-53436337	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
7	nsv912309	chr19:53092465-53440653	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
8	nsv912310	chr19:53092465-53451291	Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
9	nsv912311	chr19:53103875-53212361	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
10	nsv912312	chr19:53103875-53296371	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
11	nsv912313	chr19:53103875-53436337	ZNF genes & repeats Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
12	nsv912314	chr19:53105547-53144082	Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	9 gene(s)	inside rSNPs	diseases
13	nsv912315	chr19:53105547-53149967	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	9 gene(s)	inside rSNPs	diseases
14	nsv912316	chr19:53105547-53158023	Flanking Active TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
15	nsv912317	chr19:53105547-53440653	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
16	nsv1066762	chr19:53112568-53552217	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
17	nsv912318	chr19:53118278-53451291	Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
18	nsv458744	chr19:53120559-53236331	Genic enhancers Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer 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 target site	9 gene(s)	inside rSNPs	diseases
19	nsv580028	chr19:53120559-53236331	Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
20	esv3489404	chr19:53121944-53391394	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
21	esv3489405	chr19:53121944-53391394	Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
22	nsv1066876	chr19:53123577-53157096	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
23	nsv580029	chr19:53137583-53164172	Strong transcription Flanking Active TSS Genic enhancers Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:53139800-53142000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr19:53140200-53141200	Flanking Active TSS	Dnd41	blood
3	chr19:53140200-53142000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr19:53140200-53142000	Active TSS	GM12878-XiMat	blood
5	chr19:53140400-53141000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
6	chr19:53140400-53141000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
7	chr19:53140400-53141000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
8	chr19:53140400-53141000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr19:53140400-53141000	Flanking Active TSS	Brain Hippocampus Middle	brain
10	chr19:53140400-53141000	Flanking Active TSS	Duodenum Mucosa	Duodenum
11	chr19:53140400-53141000	Flanking Active TSS	Fetal Lung	lung
12	chr19:53140400-53141000	Enhancers	Spleen	Spleen
13	chr19:53140400-53141000	Flanking Active TSS	Osteobl	bone
14	chr19:53140400-53141200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr19:53140400-53141200	Flanking Active TSS	Primary B cells from cord blood	blood
16	chr19:53140400-53141200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
17	chr19:53140400-53141200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
18	chr19:53140400-53141200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
19	chr19:53140400-53141400	Flanking Active TSS	Primary hematopoietic stem cells	blood
20	chr19:53140400-53141400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr19:53140400-53141400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr19:53140400-53142000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr19:53140400-53142400	Active TSS	HUES6 Cell Line	embryonic stem cell
24	chr19:53140400-53142600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr19:53140600-53141000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr19:53140600-53141000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
27	chr19:53140600-53141000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
28	chr19:53140600-53141000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr19:53140600-53141000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
30	chr19:53140600-53141000	Flanking Active TSS	Colon Smooth Muscle	Colon
31	chr19:53140600-53141000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
32	chr19:53140600-53141000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
33	chr19:53140600-53141000	Flanking Active TSS	Thymus	Thymus
34	chr19:53140600-53141000	Flanking Active TSS	Hela-S3	cervix
35	chr19:53140600-53141000	Flanking Active TSS	K562	blood
36	chr19:53140600-53141000	Flanking Active TSS	NH-A	brain
37	chr19:53140600-53141200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr19:53140600-53141200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
39	chr19:53140600-53141200	Flanking Active TSS	Primary B cells from peripheral blood	blood
40	chr19:53140600-53141200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
41	chr19:53140600-53141200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr19:53140600-53141200	Flanking Active TSS	Adipose Nuclei	Adipose
43	chr19:53140600-53141200	Active TSS	Liver	Liver
44	chr19:53140600-53141200	Flanking Active TSS	Colonic Mucosa	Colon
45	chr19:53140600-53141200	Flanking Active TSS	Fetal Muscle Leg	muscle
46	chr19:53140600-53141200	Flanking Active TSS	Fetal Stomach	stomach
47	chr19:53140600-53141200	Flanking Active TSS	Fetal Thymus	thymus
48	chr19:53140600-53141200	Flanking Active TSS	Right Ventricle	heart
49	chr19:53140600-53141200	Flanking Active TSS	Stomach Smooth Muscle	stomach
50	chr19:53140600-53141200	Flanking Active TSS	HUVEC	blood vessel

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links