Variant report

Variant	rs2569517
Chromosome Location	chr19:38647654-38647655
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:38642798..38644805-chr19:38646694..38649003,2	K562	blood:
2	chr19:38645825..38649428-chr19:38653343..38656311,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000105738	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10460171	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11083447	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12460188	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12975576	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12984016	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12984380	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12984864	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12985707	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1545039	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1962866	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2004981	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2010234	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2016074	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2116862	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2163817	0.90[EUR][1000 genomes]
rs2304132	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2382972	0.88[EUR][1000 genomes]
rs2382973	0.89[EUR][1000 genomes]
rs332845	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs332846	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs332852	0.82[EUR][1000 genomes]
rs332854	0.88[EUR][1000 genomes]
rs332857	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs332859	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs332860	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs332861	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs332862	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs332863	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34646932	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35467693	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35469521	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35972455	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3852910	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3852911	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4802248	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4803805	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4803808	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67910767	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs71337549	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7253312	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7253633	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7258019	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8100956	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8107385	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs855617	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][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	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
2	nsv833821	chr19:38629937-38756792	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38600600-38652800	Weak transcription	NHDF-Ad	bronchial
2	chr19:38611000-38652800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr19:38611600-38653000	Weak transcription	HUVEC	blood vessel
4	chr19:38611800-38653000	Weak transcription	Fetal Kidney	kidney
5	chr19:38613800-38652200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr19:38613800-38652600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr19:38616000-38652600	Strong transcription	Primary B cells from peripheral blood	blood
8	chr19:38617000-38652000	Strong transcription	Fetal Intestine Small	intestine
9	chr19:38618200-38651000	Strong transcription	Fetal Intestine Large	intestine
10	chr19:38619600-38647800	Strong transcription	Fetal Stomach	stomach
11	chr19:38624400-38652400	Weak transcription	Fetal Thymus	thymus
12	chr19:38626400-38652200	Strong transcription	A549	lung
13	chr19:38627000-38652400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr19:38628400-38652600	Weak transcription	Right Atrium	heart
15	chr19:38628800-38651200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr19:38629200-38652600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr19:38629600-38651600	Strong transcription	GM12878-XiMat	blood
18	chr19:38633000-38651000	Strong transcription	Primary B cells from cord blood	blood
19	chr19:38633000-38652400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr19:38633200-38652800	Weak transcription	Colon Smooth Muscle	Colon
21	chr19:38633400-38650800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr19:38633400-38653000	Weak transcription	Fetal Brain Male	brain
23	chr19:38635400-38652600	Weak transcription	Stomach Mucosa	stomach
24	chr19:38636600-38652600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr19:38637000-38652400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr19:38637000-38652800	Weak transcription	Brain Substantia Nigra	brain
27	chr19:38638200-38667200	Strong transcription	Cortex derived primary cultured neurospheres	brain
28	chr19:38638400-38650600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr19:38641600-38652800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr19:38641800-38649800	Strong transcription	Liver	Liver
31	chr19:38642800-38650600	Strong transcription	Duodenum Smooth Muscle	Duodenum
32	chr19:38643000-38648000	Weak transcription	Brain Angular Gyrus	brain
33	chr19:38643200-38652600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr19:38643800-38647800	Weak transcription	NHLF	lung
35	chr19:38643800-38649800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr19:38643800-38650000	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr19:38643800-38650400	Strong transcription	Muscle Satellite Cultured Cells	--
38	chr19:38643800-38652600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr19:38643800-38652600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr19:38643800-38652600	Weak transcription	Small Intestine	intestine
41	chr19:38643800-38652800	Weak transcription	Left Ventricle	heart
42	chr19:38643800-38654800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr19:38644000-38647800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr19:38644000-38649800	Weak transcription	Aorta	Aorta
45	chr19:38644000-38649800	Weak transcription	Ovary	ovary
46	chr19:38644000-38652200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr19:38644000-38652400	Weak transcription	HepG2	liver
48	chr19:38644000-38652400	Weak transcription	NHEK	skin
49	chr19:38644000-38652800	Weak transcription	Placenta	Placenta
50	chr19:38644000-38659200	Weak transcription	ES-I3 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links