Variant report

Variant	rs28649029
Chromosome Location	chr15:77922318-77922319
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:77914562..77916092-chr15:77921484..77924358,2	MCF-7	breast:

Extended variants
information (count: 62 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1007538	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11852680	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11854903	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11856978	0.86[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs11856998	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11857045	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs16969013	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1877292	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1877293	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1877294	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1877295	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1877298	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1995972	0.94[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs28501538	0.96[ASN][1000 genomes]
rs28503184	0.81[AFR][1000 genomes]
rs28575171	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28575624	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28654794	0.88[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs28661259	0.86[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs28674549	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28684542	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28702901	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28720884	0.86[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs28733160	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3942665	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs56037535	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56209055	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56929920	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57354334	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60677748	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs61079432	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7165679	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7171716	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7182167	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74025322	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs74025324	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74025331	0.94[ASN][1000 genomes]
rs74025333	0.86[AFR][1000 genomes]
rs8023571	0.97[ASN][1000 genomes]
rs8024724	0.97[ASN][1000 genomes]
rs8024932	0.97[ASN][1000 genomes]
rs8026164	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8027456	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8027963	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8028788	0.81[AFR][1000 genomes]
rs9806280	0.82[AFR][1000 genomes]
rs9920101	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9920113	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9920127	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9920132	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9920134	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9920869	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9972481	0.81[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040852	chr15:77160237-78137541	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv916323	chr15:77485765-78121259	Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS 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	29 gene(s)	inside rSNPs	diseases
3	nsv833060	chr15:77816654-78035204	Weak transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	esv1806097	chr15:77817889-78301377	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	nsv904415	chr15:77845959-77943935	Weak transcription Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv904416	chr15:77845959-77967416	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv904417	chr15:77851535-77935992	Weak transcription Flanking Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv904418	chr15:77851535-77963887	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv904419	chr15:77897197-77943935	Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77910400-77923400	Weak transcription	Pancreas	Pancrea
2	chr15:77913600-77923000	Enhancers	H1 Cell Line	embryonic stem cell
3	chr15:77914400-77923200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr15:77915800-77923000	Enhancers	iPS-15b Cell Line	embryonic stem cell
5	chr15:77916600-77922800	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr15:77917200-77922400	Weak transcription	Spleen	Spleen
7	chr15:77917200-77922600	Weak transcription	Right Atrium	heart
8	chr15:77918000-77922600	Weak transcription	Fetal Lung	lung
9	chr15:77919600-77923200	Enhancers	H9 Cell Line	embryonic stem cell
10	chr15:77920600-77923000	Enhancers	iPS-20b Cell Line	embryonic stem cell
11	chr15:77921200-77922600	Enhancers	K562	blood
12	chr15:77921200-77923000	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
13	chr15:77921400-77923000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr15:77921400-77923000	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr15:77921400-77923400	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr15:77921600-77922400	Flanking Active TSS	Fetal Brain Male	brain
17	chr15:77921600-77923000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr15:77921600-77923000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr15:77921600-77923400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr15:77921800-77922400	Flanking Active TSS	Brain Angular Gyrus	brain
21	chr15:77921800-77922600	Flanking Active TSS	Brain Hippocampus Middle	brain
22	chr15:77921800-77923000	Enhancers	Brain Substantia Nigra	brain
23	chr15:77921800-77923200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr15:77921800-77923400	Flanking Active TSS	Brain Cingulate Gyrus	brain
25	chr15:77921800-77924200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr15:77921800-77924400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
27	chr15:77922000-77922400	Flanking Active TSS	Brain Anterior Caudate	brain
28	chr15:77922000-77922600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr15:77922000-77923200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr15:77922000-77923200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr15:77922000-77923800	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
32	chr15:77922000-77924000	Bivalent Enhancer	Placenta	Placenta
33	chr15:77922200-77922600	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
34	chr15:77922200-77922800	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr15:77922200-77923400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
36	chr15:77922200-77924000	Bivalent/Poised TSS	Brain Germinal Matrix	brain

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