Variant report

Variant	rs4275821
Chromosome Location	chr15:78849541-78849542
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:78832588..78837295-chr15:78846968..78850759,6	K562	blood:
2	chr15:78845755..78849755-chr15:78855790..78859263,3	K562	blood:
3	chr15:78834135..78835818-chr15:78847148..78849543,3	K562	blood:
4	chr15:78844056..78846099-chr15:78848008..78850321,3	K562	blood:
5	chr15:78848273..78850137-chr15:78854555..78857542,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000041357	Chromatin interaction
ENSG00000169684	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs11632604	0.84[CEU][hapmap]
rs11636131	0.84[CEU][hapmap]
rs11637635	0.84[CEU][hapmap];0.91[CHB][hapmap];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11858230	0.91[CEU][hapmap]
rs12591557	0.83[CEU][hapmap]
rs12902493	0.87[CEU][hapmap]
rs12906951	0.87[CEU][hapmap]
rs12907966	0.87[CEU][hapmap]
rs12910289	0.84[CEU][hapmap]
rs12914694	0.87[CEU][hapmap]
rs12916483	0.87[CEU][hapmap]
rs12916999	0.88[CEU][hapmap]
rs1504545	0.87[CEU][hapmap]
rs1504546	0.84[CEU][hapmap]
rs1979905	0.84[CEU][hapmap];0.94[YRI][hapmap]
rs1979906	0.87[CEU][hapmap];0.94[YRI][hapmap]
rs1979907	0.83[CEU][hapmap];0.89[YRI][hapmap]
rs2292117	0.87[CEU][hapmap];0.88[YRI][hapmap]
rs3813571	0.87[CEU][hapmap]
rs3813572	0.87[CEU][hapmap]
rs3829787	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4243083	0.87[CEU][hapmap]
rs471889	0.82[EUR][1000 genomes]
rs481134	0.83[CHB][hapmap];0.82[ASN][1000 genomes]
rs4886571	0.87[CEU][hapmap]
rs4887062	0.81[CEU][hapmap];0.82[YRI][hapmap]
rs4887063	0.87[CEU][hapmap];0.94[YRI][hapmap]
rs4887064	0.84[CEU][hapmap]
rs495090	0.82[EUR][1000 genomes]
rs495956	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs555018	0.82[CHB][hapmap];0.82[ASN][1000 genomes]
rs57945453	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs588765	0.90[CHB][hapmap];0.84[ASN][1000 genomes]
rs61012457	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6495306	0.83[CHB][hapmap];0.84[ASN][1000 genomes]
rs692780	0.84[CEU][hapmap];0.83[CHB][hapmap];0.82[AFR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7164030	0.84[CEU][hapmap];0.89[YRI][hapmap]
rs7173512	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8025429	0.83[CEU][hapmap];0.82[YRI][hapmap]
rs8053	0.87[CEU][hapmap];0.94[YRI][hapmap]
rs871058	0.89[EUR][1000 genomes]
rs880395	0.84[CEU][hapmap];0.89[YRI][hapmap]
rs905740	0.84[CEU][hapmap];0.89[YRI][hapmap]
rs952215	0.87[CEU][hapmap]
rs952216	0.84[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv1038816	chr15:78796434-78881087	Strong transcription Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	48 gene(s)	inside rSNPs	diseases
3	esv3311850	chr15:78848987-78850845	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
4	esv3311851	chr15:78849064-78850709	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs4275821	RP11-650L12.2	cis	Nerve Tibial	GTEx
rs4275821	RP11-650L12.2	cis	Muscle Skeletal	GTEx
rs4275821	CHRNA5	cis	lung	GTEx
rs4275821	CHRNA5	cis	Heart Left Ventricle	GTEx
rs4275821	CHRNA5	cis	Muscle Skeletal	GTEx
rs4275821	RP11-650L12.2	cis	lung	GTEx
rs4275821	CHRNA5	cis	Nerve Tibial	GTEx
rs4275821	CHRNA5	cis	Adipose Subcutaneous	GTEx
rs4275821	CHRNA5	cis	Esophagus Mucosa	GTEx
rs4275821	CHRNA3	cis	Muscle Skeletal	GTEx
rs4275821	RP11-650L12.2	cis	Heart Left Ventricle	GTEx
rs4275821	RP11-650L12.2	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78836200-78857200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr15:78841200-78856800	Weak transcription	Hela-S3	cervix
3	chr15:78842000-78857400	Weak transcription	Psoas Muscle	Psoas
4	chr15:78843000-78857200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr15:78843200-78857200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr15:78843400-78850600	Weak transcription	HepG2	liver
7	chr15:78843400-78853600	Weak transcription	K562	blood
8	chr15:78843400-78857000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr15:78843600-78852200	Weak transcription	A549	lung
10	chr15:78843600-78857400	Weak transcription	HSMM	muscle
11	chr15:78843800-78856800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr15:78843800-78857200	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr15:78843800-78857200	Weak transcription	Gastric	stomach
14	chr15:78843800-78857200	Weak transcription	Right Ventricle	heart
15	chr15:78844200-78850000	Weak transcription	Fetal Thymus	thymus
16	chr15:78844400-78849800	Weak transcription	Primary T cells from cord blood	blood
17	chr15:78844600-78857000	Weak transcription	Left Ventricle	heart
18	chr15:78847400-78857200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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