Variant report

Variant	rs61466079
Chromosome Location	chr19:41267652-41267653
allele	A/G
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:8)
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	chr19:41267623-41268789	GM12892	blood:	n/a	n/a
2	POLR2A	chr19:41267598-41268233	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr19:41267621-41268666	GM12892	blood:	n/a	n/a
4	POLR2A	chr19:41267425-41268759	HepG2	liver:	n/a	n/a
5	POLR2A	chr19:41267576-41268201	K562	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:41266506..41270324-chr19:41304182..41308237,4	MCF-7	breast:
2	chr19:41267484..41269645-chr19:41312151..41314875,2	K562	blood:
3	chr19:41265822..41267974-chr19:41269618..41272874,3	MCF-7	breast:
4	chr19:41260139..41263549-chr19:41263654..41270764,10	MCF-7	breast:
5	chr19:41264656..41268852-chr19:41282370..41284831,5	K562	blood:
6	chr19:41220988..41222886-chr19:41267608..41270115,2	MCF-7	breast:
7	chr19:41263983..41267692-chr19:41276306..41279646,3	K562	blood:
8	chr19:41224657..41226437-chr19:41266206..41269077,2	MCF-7	breast:

No data

Variant related genes	Relation type
SNRPA	TF binding region
ENSG00000268797	Chromatin interaction
ENSG00000261857	Chromatin interaction
ENSG00000123815	Chromatin interaction
ENSG00000269858	Chromatin interaction
ENSG00000077312	Chromatin interaction
ENSG00000167578	Chromatin interaction
ENSG00000171570	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10153478	0.83[AMR][1000 genomes]
rs10418304	1.00[EUR][1000 genomes]
rs10422346	1.00[EUR][1000 genomes]
rs28399441	1.00[EUR][1000 genomes]
rs28399454	1.00[EUR][1000 genomes]
rs55768417	1.00[EUR][1000 genomes]
rs56164728	1.00[EUR][1000 genomes]
rs57484466	1.00[EUR][1000 genomes]
rs7247532	1.00[EUR][1000 genomes]
rs73557121	1.00[EUR][1000 genomes]
rs8100958	1.00[EUR][1000 genomes]
rs8112043	1.00[EUR][1000 genomes]
rs8112781	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8192722	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1830682	chr19:40880127-41270055	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	139 gene(s)	inside rSNPs	diseases
2	esv1800615	chr19:41127465-41270055	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	esv1802033	chr19:41256131-41284240	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	40 gene(s)	inside rSNPs	diseases
4	esv1801805	chr19:41256581-41284363	Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	37 gene(s)	inside rSNPs	diseases
5	nsv833832	chr19:41260363-41334597	Strong transcription Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41258000-41283000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:41258800-41268400	Weak transcription	Psoas Muscle	Psoas
3	chr19:41259000-41275200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr19:41259200-41272800	Strong transcription	H1 Cell Line	embryonic stem cell
5	chr19:41260200-41272000	Strong transcription	H9 Cell Line	embryonic stem cell
6	chr19:41260400-41271800	Strong transcription	ES-I3 Cell Line	embryonic stem cell
7	chr19:41260600-41272400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr19:41260600-41272600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr19:41260600-41277200	Strong transcription	Fetal Brain Female	brain
10	chr19:41260800-41272200	Strong transcription	HUES6 Cell Line	embryonic stem cell
11	chr19:41260800-41272200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
12	chr19:41260800-41272400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr19:41260800-41272400	Strong transcription	Brain Anterior Caudate	brain
14	chr19:41260800-41283200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr19:41261000-41271800	Strong transcription	HSMM	muscle
16	chr19:41261000-41272200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr19:41261000-41272200	Strong transcription	Muscle Satellite Cultured Cells	--
18	chr19:41261200-41272200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr19:41261200-41272200	Strong transcription	Fetal Lung	lung
20	chr19:41261200-41273000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr19:41261200-41273600	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr19:41261600-41267800	Strong transcription	Cortex derived primary cultured neurospheres	brain
23	chr19:41261600-41269000	Strong transcription	Brain Hippocampus Middle	brain
24	chr19:41261600-41272000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
25	chr19:41261600-41272000	Strong transcription	Osteobl	bone
26	chr19:41261600-41272200	Strong transcription	HUES48 Cell Line	embryonic stem cell
27	chr19:41261600-41272200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr19:41261600-41275000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr19:41261600-41275200	Strong transcription	Fetal Muscle Trunk	muscle
30	chr19:41261800-41272000	Strong transcription	Ovary	ovary
31	chr19:41261800-41272200	Strong transcription	Primary hematopoietic stem cells	blood
32	chr19:41261800-41272200	Strong transcription	NHLF	lung
33	chr19:41261800-41272400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr19:41261800-41272400	Strong transcription	Fetal Intestine Large	intestine
35	chr19:41261800-41272400	Strong transcription	Skeletal Muscle Male	skeletal muscle
36	chr19:41261800-41272600	Strong transcription	Right Ventricle	heart
37	chr19:41261800-41276800	Strong transcription	Fetal Intestine Small	intestine
38	chr19:41261800-41278200	Strong transcription	Fetal Stomach	stomach
39	chr19:41261800-41282800	Weak transcription	Right Atrium	heart
40	chr19:41262000-41270000	Weak transcription	Fetal Heart	heart
41	chr19:41262000-41272200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr19:41262000-41272200	Strong transcription	K562	blood
43	chr19:41262000-41273400	Strong transcription	Brain Germinal Matrix	brain
44	chr19:41262000-41276200	Strong transcription	Thymus	Thymus
45	chr19:41262200-41273800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr19:41262400-41270400	Strong transcription	Fetal Thymus	thymus
47	chr19:41262400-41272400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr19:41262400-41273000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr19:41262600-41271800	Strong transcription	Fetal Kidney	kidney
50	chr19:41262600-41272000	Strong transcription	Brain Angular Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links