Variant report

Variant	rs28625002
Chromosome Location	chr19:38482289-38482290
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:38481842..38483998-chr19:38488406..38490130,2	K562	blood:
2	chr19:38480879..38483750-chr19:38494788..38496320,2	MCF-7	breast:
3	chr19:38470130..38474074-chr19:38479565..38484723,5	MCF-7	breast:
4	chr19:38457253..38459371-chr19:38481407..38483076,2	MCF-7	breast:
5	chr19:38395223..38398524-chr19:38481213..38484062,6	MCF-7	breast:
6	chr19:38421711..38424524-chr19:38480296..38482978,4	MCF-7	breast:
7	chr19:38393241..38399415-chr19:38476540..38485383,15	MCF-7	breast:
8	chr19:38479835..38482339-chr19:38571881..38574395,2	MCF-7	breast:
9	chr19:38407792..38410171-chr19:38481203..38483917,2	MCF-7	breast:
10	chr19:38472927..38474902-chr19:38482178..38484229,2	K562	blood:
11	chr19:38431713..38434433-chr19:38480033..38484198,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000105738	Chromatin interaction
ENSG00000171804	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10401835	1.00[EUR][1000 genomes]
rs10404447	1.00[EUR][1000 genomes]
rs10405162	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10405381	1.00[EUR][1000 genomes]
rs10406765	1.00[EUR][1000 genomes]
rs10407169	1.00[EUR][1000 genomes]
rs10407230	1.00[EUR][1000 genomes]
rs10407370	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10407806	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10408169	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10410961	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10413138	1.00[EUR][1000 genomes]
rs10413551	1.00[EUR][1000 genomes]
rs10413596	1.00[EUR][1000 genomes]
rs10413865	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10414605	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10414916	1.00[EUR][1000 genomes]
rs10414927	1.00[EUR][1000 genomes]
rs10415289	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10415809	1.00[EUR][1000 genomes]
rs10418855	1.00[AMR][1000 genomes]
rs10419299	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10419700	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10419708	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10419753	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10420885	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10423429	1.00[EUR][1000 genomes]
rs10424104	1.00[EUR][1000 genomes]
rs10424626	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10424818	1.00[EUR][1000 genomes]
rs10425099	1.00[EUR][1000 genomes]
rs10425571	1.00[EUR][1000 genomes]
rs13343460	1.00[EUR][1000 genomes]
rs28376501	1.00[EUR][1000 genomes]
rs28380555	1.00[EUR][1000 genomes]
rs28421402	1.00[EUR][1000 genomes]
rs28516776	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28540039	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28627637	1.00[EUR][1000 genomes]
rs28637743	1.00[EUR][1000 genomes]
rs28649033	1.00[EUR][1000 genomes]
rs28660098	1.00[EUR][1000 genomes]
rs28700884	1.00[EUR][1000 genomes]
rs56134404	1.00[EUR][1000 genomes]
rs56216562	1.00[EUR][1000 genomes]
rs58260561	1.00[EUR][1000 genomes]
rs59501312	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59571293	1.00[EUR][1000 genomes]
rs61456950	1.00[EUR][1000 genomes]
rs71354969	1.00[EUR][1000 genomes]
rs73630898	1.00[EUR][1000 genomes]
rs73632925	1.00[EUR][1000 genomes]
rs73930357	1.00[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38461600-38493600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr19:38461600-38493600	Weak transcription	Stomach Smooth Muscle	stomach
3	chr19:38463800-38484800	Weak transcription	Fetal Stomach	stomach
4	chr19:38468200-38483600	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr19:38470800-38494000	Weak transcription	Right Ventricle	heart
6	chr19:38471200-38493800	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr19:38471400-38483600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr19:38471400-38488600	Weak transcription	NHLF	lung
9	chr19:38472400-38493800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr19:38472800-38489600	Weak transcription	Fetal Kidney	kidney
11	chr19:38473200-38482600	Weak transcription	HSMM	muscle
12	chr19:38473200-38488600	Weak transcription	HSMMtube	muscle
13	chr19:38474800-38513600	Weak transcription	Gastric	stomach
14	chr19:38475000-38488600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr19:38475800-38488600	Weak transcription	Hela-S3	cervix
16	chr19:38476400-38482800	Enhancers	H1 Cell Line	embryonic stem cell
17	chr19:38476400-38484800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr19:38476800-38482800	Enhancers	H9 Cell Line	embryonic stem cell
19	chr19:38476800-38482800	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr19:38476800-38483800	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr19:38477200-38483000	Enhancers	ES-I3 Cell Line	embryonic stem cell
22	chr19:38477200-38483800	Enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr19:38477200-38488800	Weak transcription	Brain Anterior Caudate	brain
24	chr19:38477400-38491800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr19:38477600-38493800	Weak transcription	Thymus	Thymus
26	chr19:38478000-38483800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr19:38478000-38483800	Genic enhancers	A549	lung
28	chr19:38478200-38482400	Enhancers	HUES64 Cell Line	embryonic stem cell
29	chr19:38478200-38482800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr19:38478200-38482800	Enhancers	Placenta	Placenta
31	chr19:38478200-38483800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr19:38478600-38483400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr19:38478800-38482400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr19:38479200-38493800	Weak transcription	Colonic Mucosa	Colon
35	chr19:38479600-38483000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr19:38479600-38485400	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr19:38479800-38483400	Genic enhancers	Primary B cells from peripheral blood	blood
38	chr19:38479800-38484800	Weak transcription	Primary T cells from cord blood	blood
39	chr19:38479800-38488600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr19:38479800-38489800	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr19:38480000-38485400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr19:38480000-38488600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr19:38480000-38493600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr19:38480000-38493600	Weak transcription	Primary hematopoietic stem cells	blood
45	chr19:38480000-38493800	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr19:38480200-38482400	Enhancers	Skeletal Muscle Male	skeletal muscle
47	chr19:38480200-38483000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr19:38480200-38489800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr19:38480400-38482400	Enhancers	Psoas Muscle	Psoas
50	chr19:38480400-38482400	Enhancers	Skeletal Muscle Female	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links