Variant report

Variant	rs369009
Chromosome Location	chr19:53087024-53087025
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	chr19:53086723-53087881	K562	blood:	n/a	n/a
2	POLR2A	chr19:53086829-53087422	GM12891	blood:	n/a	n/a
3	POLR2A	chr19:53086790-53087472	GM12891	blood:	n/a	n/a
4	POLR2A	chr19:53086872-53087130	GM12891	blood:	n/a	n/a
5	POLR2A	chr19:53086869-53087516	GM12892	blood:	n/a	n/a
6	POLR2A	chr19:53086793-53087421	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:53073504..53075016-chr19:53086712..53089202,2	MCF-7	breast:
2	chr19:53085553..53087688-chr19:53089270..53091312,2	MCF-7	breast:
3	chr19:53086321..53088746-chr19:53090945..53093130,2	K562	blood:

Variant related genes	Relation type
ZNF137P	TF binding region
ENSG00000123870	Chromatin interaction
ENSG00000167562	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs368683	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs374395	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs45586042	0.87[EUR][1000 genomes]
rs544769	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs544869	0.82[ASN][1000 genomes]
rs599859	1.00[ASN][1000 genomes]
rs62117246	0.89[EUR][1000 genomes]
rs62117248	0.89[EUR][1000 genomes]
rs62117249	0.89[EUR][1000 genomes]
rs650750	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs661876	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8105873	0.89[EUR][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	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	nsv978841	chr19:52983057-53088237	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv510772	chr19:53037211-53103470	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1065584	chr19:53043126-53127459	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	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
6	nsv458743	chr19:53065661-53114267	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv580027	chr19:53065661-53114267	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv912304	chr19:53071155-53114267	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	esv3385321	chr19:53086990-53090388	ZNF genes & repeats Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:53074200-53087800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:53074600-53087400	Weak transcription	Fetal Heart	heart
3	chr19:53074600-53088000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr19:53074600-53103600	Weak transcription	Fetal Brain Male	brain
5	chr19:53075400-53089600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr19:53075400-53092200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr19:53075400-53092400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr19:53075400-53092400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
9	chr19:53075600-53087800	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr19:53075800-53087400	Strong transcription	Osteobl	bone
11	chr19:53075800-53088000	Strong transcription	Rectal Smooth Muscle	rectum
12	chr19:53076400-53096000	Strong transcription	Dnd41	blood
13	chr19:53077600-53088000	Strong transcription	Fetal Brain Female	brain
14	chr19:53079200-53087400	Strong transcription	Brain Anterior Caudate	brain
15	chr19:53079200-53087800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
16	chr19:53079200-53092200	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr19:53079400-53087400	Strong transcription	Brain Germinal Matrix	brain
18	chr19:53079400-53087600	Strong transcription	Brain Inferior Temporal Lobe	brain
19	chr19:53079400-53087600	Strong transcription	Skeletal Muscle Male	skeletal muscle
20	chr19:53079400-53088000	Strong transcription	H1 Cell Line	embryonic stem cell
21	chr19:53079400-53089400	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
22	chr19:53079400-53090400	ZNF genes & repeats	Liver	Liver
23	chr19:53079400-53092200	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
24	chr19:53079400-53094200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
25	chr19:53079400-53096000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
26	chr19:53079600-53089600	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr19:53079600-53091800	ZNF genes & repeats	Thymus	Thymus
28	chr19:53079800-53089200	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
29	chr19:53079800-53091000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr19:53080200-53089400	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
31	chr19:53081600-53087200	Strong transcription	Muscle Satellite Cultured Cells	--
32	chr19:53081600-53088400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr19:53081600-53090200	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
34	chr19:53082200-53089200	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
35	chr19:53082800-53089200	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
36	chr19:53083200-53087400	Strong transcription	Fetal Muscle Trunk	muscle
37	chr19:53083200-53087600	Strong transcription	Left Ventricle	heart
38	chr19:53083200-53091000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr19:53083400-53087400	Strong transcription	Stomach Smooth Muscle	stomach
40	chr19:53083400-53088000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr19:53083400-53088800	ZNF genes & repeats	Primary B cells from peripheral blood	blood
42	chr19:53083400-53089200	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
43	chr19:53083400-53090400	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
44	chr19:53083400-53091000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr19:53083600-53087200	Strong transcription	HUES6 Cell Line	embryonic stem cell
46	chr19:53083600-53087400	Strong transcription	Brain Substantia Nigra	brain
47	chr19:53083600-53087600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr19:53083600-53087600	Strong transcription	Adipose Nuclei	Adipose
49	chr19:53083600-53087600	Strong transcription	Fetal Lung	lung
50	chr19:53083600-53087600	Strong transcription	Gastric	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links