Variant report

Variant	rs10419307
Chromosome Location	chr19:19104026-19104027
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:19103470-19104058	K562	blood:	n/a	n/a
2	POLR2A	chr19:19103570-19104145	PANC-1	pancreas:	n/a	n/a
3	POLR2A	chr19:19104019-19104048	Hela-S3	cervix:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:19099305..19102487-chr19:19102568..19107094,5	MCF-7	breast:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ARMC6-1	chr19:19103397-19104419	ENSG00000245755
2	lnc-ARMC6-1	chr19:19103397-19104419	ENSG00000269131.1

No data

Variant related genes	Relation type
SUGP2	TF binding region
ENSG00000064607	Chromatin interaction
ENSG00000269131	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10402553	1.00[EUR][1000 genomes]
rs10403808	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10404020	0.83[AFR][1000 genomes]
rs10404077	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10404860	1.00[EUR][1000 genomes]
rs10404879	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10405178	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10405609	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10406282	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10406341	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10406496	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10407260	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10407753	0.93[AFR][1000 genomes]
rs10407980	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10408567	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10409265	0.88[AFR][1000 genomes]
rs10409395	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10411786	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10412101	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10413216	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10414535	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10415998	0.88[AFR][1000 genomes]
rs10416041	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10416054	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10416240	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10416250	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10416730	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10417310	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10417682	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10417995	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10418688	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10419114	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10420479	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10420559	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10422058	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10422079	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10422238	0.84[AFR][1000 genomes]
rs10422813	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10423129	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10426131	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs13344769	1.00[EUR][1000 genomes]
rs13344835	0.88[AFR][1000 genomes]
rs13345246	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28369262	0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28374656	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28376498	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28380085	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28421315	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28445835	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28475392	0.83[AFR][1000 genomes]
rs28477157	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28477961	1.00[AFR][1000 genomes]
rs28507927	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28533991	0.86[AFR][1000 genomes]
rs28568599	1.00[EUR][1000 genomes]
rs28582808	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28619464	0.95[AFR][1000 genomes]
rs28628081	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28699197	0.83[AFR][1000 genomes]
rs28720008	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35646935	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs57654710	1.00[EUR][1000 genomes]
rs6511012	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7252085	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7256152	1.00[EUR][1000 genomes]
rs8106189	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9917000	1.00[EUR][1000 genomes]
rs9917034	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833778	chr19:19012669-19201487	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
2	nsv2435	chr19:19077432-19122579	Strong transcription Bivalent Enhancer Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 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	chr19:19084200-19107800	Weak transcription	Right Atrium	heart
2	chr19:19098000-19106600	Weak transcription	Fetal Kidney	kidney
3	chr19:19098200-19104600	Weak transcription	Stomach Mucosa	stomach
4	chr19:19098600-19109800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr19:19099400-19105400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr19:19100200-19105800	Strong transcription	Brain Inferior Temporal Lobe	brain
7	chr19:19100200-19117400	Strong transcription	Fetal Intestine Small	intestine
8	chr19:19100600-19106000	Strong transcription	Fetal Intestine Large	intestine
9	chr19:19100600-19122800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr19:19100800-19106400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr19:19100800-19106400	Strong transcription	Fetal Muscle Trunk	muscle
12	chr19:19100800-19106600	Strong transcription	Fetal Muscle Leg	muscle
13	chr19:19101000-19105600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr19:19101000-19105600	Strong transcription	Fetal Stomach	stomach
15	chr19:19101000-19105800	Strong transcription	Brain Hippocampus Middle	brain
16	chr19:19101000-19106400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr19:19101000-19106400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr19:19101000-19106400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr19:19101000-19107200	Strong transcription	Esophagus	oesophagus
20	chr19:19101000-19109400	Strong transcription	Lung	lung
21	chr19:19101000-19109800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr19:19101000-19114000	Weak transcription	Small Intestine	intestine
23	chr19:19101000-19125600	Strong transcription	Thymus	Thymus
24	chr19:19101000-19133000	Strong transcription	Fetal Thymus	thymus
25	chr19:19101200-19106000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr19:19101200-19106200	Strong transcription	Stomach Smooth Muscle	stomach
27	chr19:19101200-19106400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
28	chr19:19101200-19106400	Strong transcription	Brain Substantia Nigra	brain
29	chr19:19101200-19108200	Strong transcription	Primary T cells fromperipheralblood	blood
30	chr19:19101200-19108400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr19:19101200-19108400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr19:19101200-19109400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr19:19101200-19109800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
34	chr19:19101200-19109800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr19:19101200-19110400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr19:19101200-19126000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr19:19101200-19130400	Strong transcription	Duodenum Mucosa	Duodenum
38	chr19:19101200-19140200	Strong transcription	Primary neutrophils fromperipheralblood	blood
39	chr19:19101400-19105800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr19:19101400-19106200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr19:19101400-19106200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr19:19101400-19106200	Strong transcription	Placenta	Placenta
43	chr19:19101400-19106200	Strong transcription	NHDF-Ad	bronchial
44	chr19:19101400-19106400	Strong transcription	Osteobl	bone
45	chr19:19101400-19106800	Strong transcription	Skeletal Muscle Male	skeletal muscle
46	chr19:19101400-19109800	Strong transcription	Liver	Liver
47	chr19:19101400-19113000	Strong transcription	Skeletal Muscle Female	skeletal muscle
48	chr19:19101400-19130400	Strong transcription	Primary monocytes fromperipheralblood	blood
49	chr19:19101400-19142000	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chr19:19101600-19106400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links