Variant report

Variant	rs28470809
Chromosome Location	chr15:59036258-59036259
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:58841936..58843699-chr15:59035411..59037859,2	MCF-7	breast:
2	chr15:59030373..59033312-chr15:59035023..59037730,3	MCF-7	breast:
3	chr15:59033587..59035480-chr15:59035555..59037744,3	K562	blood:
4	chr15:59030650..59032606-chr15:59033863..59036396,2	K562	blood:
5	chr15:59021059..59023749-chr15:59034779..59037397,2	K562	blood:

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

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs11071397	0.81[AMR][1000 genomes]
rs12437952	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12437998	0.81[AMR][1000 genomes]
rs12439231	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12439632	0.81[AMR][1000 genomes]
rs12440267	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12441313	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12441912	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12591310	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12595057	0.82[AMR][1000 genomes]
rs12900343	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12905110	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12908261	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12910927	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12912327	0.84[AMR][1000 genomes]
rs12913383	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12917083	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1426652	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17236194	0.80[AFR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17301954	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1820480	0.81[AMR][1000 genomes]
rs2013098	0.81[AMR][1000 genomes]
rs2052805	0.83[AMR][1000 genomes]
rs2414608	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28394222	0.81[AMR][1000 genomes]
rs28412567	0.81[AMR][1000 genomes]
rs28455654	0.83[AMR][1000 genomes]
rs28470867	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs28489732	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28510910	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28536555	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28549001	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28733370	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28793354	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28818840	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28876251	0.81[AMR][1000 genomes]
rs28889637	0.81[AMR][1000 genomes]
rs35956992	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6494034	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6494038	0.84[EUR][1000 genomes]
rs7163939	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7165019	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7168825	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7169205	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7169796	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8029805	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8033691	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051058	chr15:58519922-59092530	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv542401	chr15:58519922-59092530	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	esv34110	chr15:58949991-59381634	Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
4	esv1843037	chr15:59005922-59115159	Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
5	esv1826703	chr15:59005922-59213678	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats 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	44 gene(s)	inside rSNPs	diseases
6	esv1798487	chr15:59027139-59213678	Strong transcription Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
7	nsv428638	chr15:59032300-59126567	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:58977200-59039200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr15:59022200-59040200	Weak transcription	Fetal Muscle Trunk	muscle
3	chr15:59022600-59038600	Weak transcription	Fetal Brain Female	brain
4	chr15:59023600-59040000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
5	chr15:59024000-59038200	Weak transcription	Fetal Stomach	stomach
6	chr15:59025600-59038200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr15:59025600-59038200	Weak transcription	Gastric	stomach
8	chr15:59025600-59040000	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr15:59026800-59039600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
10	chr15:59027000-59039800	Enhancers	Primary T helper cells fromperipheralblood	blood
11	chr15:59027600-59037800	Weak transcription	Fetal Intestine Small	intestine
12	chr15:59027600-59038000	Weak transcription	Fetal Intestine Large	intestine
13	chr15:59027600-59040200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr15:59030600-59037800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr15:59030800-59037800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr15:59030800-59038200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr15:59030800-59038400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr15:59030800-59039400	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr15:59031000-59039200	Weak transcription	Duodenum Mucosa	Duodenum
20	chr15:59031200-59037800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr15:59031200-59037800	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr15:59031400-59037800	Weak transcription	Hela-S3	cervix
23	chr15:59031400-59037800	Weak transcription	NHEK	skin
24	chr15:59032200-59036800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
25	chr15:59032200-59038400	Weak transcription	Aorta	Aorta
26	chr15:59032400-59036800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
27	chr15:59032600-59037800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr15:59032600-59038000	Weak transcription	Brain Cingulate Gyrus	brain
29	chr15:59032600-59038400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr15:59033000-59038800	Weak transcription	Primary B cells from cord blood	blood
31	chr15:59033200-59037000	Enhancers	iPS-15b Cell Line	embryonic stem cell
32	chr15:59033400-59037200	Enhancers	Brain Substantia Nigra	brain
33	chr15:59033400-59038200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr15:59033400-59039000	Enhancers	Brain Hippocampus Middle	brain
35	chr15:59033600-59036400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr15:59033600-59036600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
37	chr15:59033600-59036800	Enhancers	iPS-20b Cell Line	embryonic stem cell
38	chr15:59033600-59040000	Enhancers	Primary T helper naive cells from peripheral blood	blood
39	chr15:59033600-59040400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
40	chr15:59033800-59038200	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr15:59034000-59037000	Enhancers	Brain Anterior Caudate	brain
42	chr15:59034000-59037400	Enhancers	Primary monocytes fromperipheralblood	blood
43	chr15:59034200-59036400	Enhancers	Brain Germinal Matrix	brain
44	chr15:59034400-59037000	Enhancers	HUES6 Cell Line	embryonic stem cell
45	chr15:59034400-59039200	Enhancers	HUES64 Cell Line	embryonic stem cell
46	chr15:59034600-59036400	Enhancers	ES-I3 Cell Line	embryonic stem cell
47	chr15:59034600-59036400	Enhancers	H1 Cell Line	embryonic stem cell
48	chr15:59034600-59037000	Enhancers	HUES48 Cell Line	embryonic stem cell
49	chr15:59034600-59038000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr15:59034800-59036800	Enhancers	iPS-18 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links