Variant report

Variant	rs28368579
Chromosome Location	chr15:77895482-77895483
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:77890507..77893828-chr15:77894009..77899298,4	MCF-7	breast:
2	chr15:77895225..77896761-chr15:77915510..77917012,2	K562	blood:
3	chr15:77894564..77896146-chr15:77898435..77900182,2	K562	blood:
4	chr15:77891327..77896574-chr15:77898422..77902980,9	K562	blood:

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11631894	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11636780	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11638351	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11638674	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16968998	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16968999	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28477219	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28706124	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4286073	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4886882	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4886884	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4886885	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4886886	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4886887	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4886888	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7171141	0.86[EUR][1000 genomes]
rs884527	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9806139	0.98[AMR][1000 genomes];0.98[EUR][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	nsv1036749	chr15:77884026-77912408	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28368579	TSPAN3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77883800-77896000	Weak transcription	Brain Hippocampus Middle	brain
2	chr15:77889400-77896000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr15:77889800-77896400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr15:77891000-77896600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr15:77891000-77898800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr15:77892200-77897200	Weak transcription	Gastric	stomach
7	chr15:77892200-77897600	Weak transcription	Right Ventricle	heart
8	chr15:77892400-77896000	Weak transcription	Fetal Brain Male	brain
9	chr15:77892400-77896200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr15:77892400-77896800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr15:77892400-77896800	Weak transcription	Lung	lung
12	chr15:77892400-77897000	Weak transcription	Right Atrium	heart
13	chr15:77892600-77896000	Weak transcription	Brain Substantia Nigra	brain
14	chr15:77892800-77896000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr15:77892800-77896000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr15:77892800-77896400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr15:77892800-77896600	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr15:77892800-77897000	Weak transcription	Fetal Thymus	thymus
19	chr15:77892800-77897200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr15:77893000-77895800	Weak transcription	Left Ventricle	heart
21	chr15:77893000-77896200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr15:77893000-77896200	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr15:77893000-77896200	Weak transcription	Fetal Stomach	stomach
24	chr15:77893000-77896400	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr15:77893000-77896400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr15:77893000-77896600	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr15:77893000-77896800	Weak transcription	Stomach Smooth Muscle	stomach
28	chr15:77893200-77896200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr15:77893200-77897200	Weak transcription	K562	blood
30	chr15:77893400-77895800	Weak transcription	Fetal Heart	heart
31	chr15:77894000-77896400	Weak transcription	Spleen	Spleen
32	chr15:77895000-77895800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr15:77895000-77898600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links