Variant report

Variant	rs28444683
Chromosome Location	chr15:78984507-78984508
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:78983812..78985475-chr15:79007336..79009142,2	MCF-7	breast:
2	chr15:78977969..78980271-chr15:78982460..78985285,2	K562	blood:
3	chr15:78983381..78985912-chr15:78992265..78995147,2	MCF-7	breast:

Extended variants
information (count: 32 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs12324870	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12901241	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12901331	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12905641	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12910237	0.84[ASN][1000 genomes]
rs12915539	0.82[ASN][1000 genomes]
rs34067845	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34099810	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34275594	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34422348	0.91[AMR][1000 genomes]
rs34550457	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34694149	0.86[EUR][1000 genomes]
rs35701817	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35704045	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs58526289	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs58946838	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61630816	0.86[EUR][1000 genomes]
rs62010555	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62010556	0.82[AMR][1000 genomes]
rs67775542	0.82[AMR][1000 genomes]
rs7169223	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7178007	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8038920	0.84[EUR][1000 genomes]
rs922691	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917303	chr15:78491050-79205255	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	122 gene(s)	inside rSNPs	diseases
2	nsv1045827	chr15:78907656-79004642	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv457208	chr15:78908032-79019610	Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv570201	chr15:78908032-79019610	Bivalent Enhancer Bivalent/Poised TSS Strong transcription Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv974713	chr15:78945824-78996783	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv457209	chr15:78949127-78986805	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv471256	chr15:78949127-78986805	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv570203	chr15:78949127-78986805	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs28444683	CHRNA5	cis	Muscle Skeletal	GTEx
rs28444683	CHRNA3	cis	Muscle Skeletal	GTEx
rs28444683	RP11-650L12.2	cis	Muscle Skeletal	GTEx

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78978400-78984600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr15:78978400-78984600	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr15:78978600-78985400	Weak transcription	Fetal Brain Female	brain
4	chr15:78979000-78985000	Weak transcription	Thymus	Thymus
5	chr15:78979000-78988400	Weak transcription	Left Ventricle	heart
6	chr15:78979200-78985000	Weak transcription	Fetal Thymus	thymus
7	chr15:78983200-78984600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr15:78983200-78984600	Enhancers	Spleen	Spleen
9	chr15:78983200-78984800	Enhancers	HUES6 Cell Line	embryonic stem cell
10	chr15:78983400-78985200	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr15:78983600-78984600	Enhancers	H1 Cell Line	embryonic stem cell
12	chr15:78983600-78984600	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr15:78983600-78984600	Enhancers	Esophagus	oesophagus
14	chr15:78983600-78984600	Enhancers	Fetal Muscle Trunk	muscle
15	chr15:78983600-78984600	Bivalent Enhancer	Fetal Muscle Leg	muscle
16	chr15:78983600-78984800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr15:78983600-78988800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr15:78983800-78984800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr15:78983800-78985000	Enhancers	ES-I3 Cell Line	embryonic stem cell
20	chr15:78984000-78985200	Enhancers	iPS-15b Cell Line	embryonic stem cell
21	chr15:78984000-78988200	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr15:78984200-78984600	Enhancers	Fetal Stomach	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links