Variant report

Variant	rs277978
Chromosome Location	chr5:70926559-70926560
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:70924678..70928515-chr5:71047455..71049125,3	MCF-7	breast:
2	chr5:70926230..70927749-chr5:70936129..70937850,2	K562	blood:
3	chr5:70920053..70922603-chr5:70926278..70929720,3	K562	blood:
4	chr5:70882995..70885167-chr5:70926126..70927669,2	K562	blood:

Variant related genes	Relation type
ENSG00000131844	Chromatin interaction

Extended variants
information (count: 102 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs10942466	0.83[AMR][1000 genomes]
rs10942683	0.90[AMR][1000 genomes]
rs13158264	0.84[AMR][1000 genomes]
rs157044	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs157046	0.81[AMR][1000 genomes]
rs157049	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1693895	0.81[AMR][1000 genomes]
rs1698063	0.82[AMR][1000 genomes]
rs175872	0.83[AMR][1000 genomes]
rs182190	0.84[AMR][1000 genomes]
rs185733	0.81[AMR][1000 genomes]
rs190692	0.87[AMR][1000 genomes]
rs2646639	0.87[AMR][1000 genomes]
rs276592	0.84[AMR][1000 genomes]
rs276597	0.83[AMR][1000 genomes]
rs276598	0.89[AMR][1000 genomes]
rs276600	0.84[AMR][1000 genomes]
rs276601	0.90[AMR][1000 genomes]
rs277936	0.85[EUR][1000 genomes]
rs277939	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs277940	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs277942	0.80[AMR][1000 genomes]
rs277944	0.80[AMR][1000 genomes]
rs277945	0.81[AMR][1000 genomes]
rs277954	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs277957	0.81[AMR][1000 genomes]
rs277958	0.81[AMR][1000 genomes]
rs277960	0.81[AMR][1000 genomes]
rs277962	0.81[AMR][1000 genomes]
rs277963	0.81[AMR][1000 genomes]
rs277964	0.81[AMR][1000 genomes]
rs277965	0.81[AMR][1000 genomes]
rs277966	0.85[AMR][1000 genomes]
rs277967	0.83[AMR][1000 genomes]
rs277976	0.85[EUR][1000 genomes]
rs277979	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs277980	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs277981	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs277985	0.88[ASN][1000 genomes]
rs277986	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs277996	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs277999	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs278000	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs278001	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs279291	0.84[AMR][1000 genomes]
rs279322	0.85[AMR][1000 genomes]
rs279337	0.81[AMR][1000 genomes]
rs35327154	0.81[AMR][1000 genomes]
rs36036841	0.82[AMR][1000 genomes]
rs3761965	0.82[AMR][1000 genomes]
rs378585	0.81[AMR][1000 genomes]
rs384732	0.87[AMR][1000 genomes]
rs3890749	0.82[AMR][1000 genomes]
rs392791	0.87[AMR][1000 genomes]
rs410776	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs418738	0.82[AMR][1000 genomes]
rs451229	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs456938	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs457908	0.81[AMR][1000 genomes]
rs458009	0.81[AMR][1000 genomes]
rs458150	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs458370	0.81[AMR][1000 genomes]
rs459298	0.81[AMR][1000 genomes]
rs459787	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs460778	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs461215	0.81[AMR][1000 genomes]
rs462282	0.81[AMR][1000 genomes]
rs463871	0.81[AMR][1000 genomes]
rs464182	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs464594	0.81[AMR][1000 genomes]
rs464962	0.81[AMR][1000 genomes]
rs465073	0.81[AMR][1000 genomes]
rs466930	0.81[AMR][1000 genomes]
rs467160	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs467413	0.81[AMR][1000 genomes]
rs467563	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs467620	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs467851	0.81[AMR][1000 genomes]
rs467901	0.83[AMR][1000 genomes]
rs468028	0.81[AMR][1000 genomes]
rs468033	0.81[AMR][1000 genomes]
rs468128	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs468158	0.81[AMR][1000 genomes]
rs468446	0.81[AMR][1000 genomes]
rs468467	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs468564	0.81[AMR][1000 genomes]
rs468633	0.81[AMR][1000 genomes]
rs468658	0.81[AMR][1000 genomes]
rs468776	0.81[AMR][1000 genomes]
rs468832	0.81[AMR][1000 genomes]
rs469039	0.81[AMR][1000 genomes]
rs469369	0.81[AMR][1000 genomes]
rs469548	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4704096	0.81[AMR][1000 genomes]
rs541035	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs544779	0.85[EUR][1000 genomes]
rs62361813	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6885523	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9791120	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034703	chr5:70391173-70995695	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv830340	chr5:70797113-70967110	Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers 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	10 gene(s)	inside rSNPs	diseases
3	nsv532805	chr5:70916228-71020967	Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs277978	BDP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:70884800-70934800	Weak transcription	Fetal Brain Male	brain
2	chr5:70893600-70930200	Weak transcription	Rectal Smooth Muscle	rectum
3	chr5:70895800-70937800	Weak transcription	Colonic Mucosa	Colon
4	chr5:70897200-70930000	Weak transcription	Psoas Muscle	Psoas
5	chr5:70897400-70933800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr5:70897800-70944800	Weak transcription	Small Intestine	intestine
7	chr5:70898200-70944200	Weak transcription	Osteobl	bone
8	chr5:70898400-70935400	Weak transcription	NHDF-Ad	bronchial
9	chr5:70898400-70955000	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr5:70898600-70948400	Weak transcription	Brain Germinal Matrix	brain
11	chr5:70900000-70944800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr5:70900200-70928200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr5:70900200-70930800	Weak transcription	HMEC	breast
14	chr5:70900200-70945200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr5:70900400-70927000	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr5:70900400-70927600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr5:70900400-70927800	Weak transcription	Brain Substantia Nigra	brain
18	chr5:70900400-70931000	Weak transcription	K562	blood
19	chr5:70900400-70933200	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr5:70906600-70952400	Weak transcription	Stomach Mucosa	stomach
21	chr5:70907200-70927000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr5:70907200-70928200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr5:70907400-70932800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr5:70907600-70928000	Weak transcription	Fetal Lung	lung
25	chr5:70908800-70927200	Weak transcription	Thymus	Thymus
26	chr5:70909000-70938200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr5:70909200-70931000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr5:70911200-70928000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr5:70912200-70931000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr5:70912400-70927000	Weak transcription	Brain Angular Gyrus	brain
31	chr5:70912400-70936600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr5:70912600-70927800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr5:70912600-70941800	Weak transcription	Colon Smooth Muscle	Colon
34	chr5:70912600-70943800	Weak transcription	A549	lung
35	chr5:70912800-70927000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr5:70913000-70927000	Weak transcription	Pancreas	Pancrea
37	chr5:70913000-70928000	Weak transcription	Brain Anterior Caudate	brain
38	chr5:70913000-70934200	Weak transcription	Fetal Brain Female	brain
39	chr5:70913200-70927000	Weak transcription	NHEK	skin
40	chr5:70913200-70928200	Weak transcription	Brain Cingulate Gyrus	brain
41	chr5:70914200-70930400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr5:70914200-70938000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr5:70914200-70948800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr5:70915400-70950800	Weak transcription	NHLF	lung
45	chr5:70917000-70927800	Weak transcription	Placenta	Placenta
46	chr5:70917000-70928000	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr5:70917000-70928200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr5:70917000-70928200	Weak transcription	Ovary	ovary
49	chr5:70917000-70936400	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr5:70917000-70945000	Weak transcription	Hela-S3	cervix

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links