Variant report

Variant	rs692780
Chromosome Location	chr15:78876505-78876506
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:78875274..78876810-chr15:78879173..78881083,2	K562	blood:
2	chr15:78875377..78879789-chr15:78880777..78885451,4	MCF-7	breast:
3	chr15:78875573..78878455-chr15:78878955..78880696,2	K562	blood:
4	chr15:78874644..78876523-chr15:78887781..78889703,2	MCF-7	breast:
5	chr15:78856829..78859246-chr15:78874594..78877162,2	K562	blood:
6	chr15:78874935..78877204-chr15:78886977..78889217,2	K562	blood:

Variant related genes	Relation type
ENSG00000080644	Chromatin interaction
ENSG00000169684	Chromatin interaction
ENSG00000261762	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11637635	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11858230	0.82[CEU][hapmap]
rs12916999	0.80[CEU][hapmap]
rs17408276	0.96[CEU][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2067808	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2456019	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2869546	0.92[CEU][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3743073	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3743074	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3743075	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3743077	0.83[CEU][hapmap]
rs3829787	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4275821	0.84[CEU][hapmap];0.83[CHB][hapmap];0.82[AFR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs471889	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs472054	0.96[CEU][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs481134	0.88[CEU][hapmap];0.82[CHB][hapmap];0.85[YRI][hapmap];0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs495090	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs495956	1.00[CEU][hapmap];0.91[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs514743	0.96[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs555018	0.84[CEU][hapmap];0.82[CHB][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs57945453	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs584135	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs588765	0.87[CEU][hapmap];0.90[CHB][hapmap];0.83[YRI][hapmap];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs601079	0.85[CEU][hapmap];0.82[JPT][hapmap]
rs61012457	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs615470	0.96[CEU][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62010327	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62010328	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs621849	0.88[CEU][hapmap];0.82[JPT][hapmap]
rs647041	0.81[CEU][hapmap];0.84[AMR][1000 genomes]
rs6495306	0.88[CEU][hapmap];0.82[CHB][hapmap];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6495307	0.81[CEU][hapmap]
rs660652	0.96[CEU][hapmap];0.81[YRI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs680244	0.88[CEU][hapmap];0.82[JPT][hapmap]
rs7173512	0.84[CEU][hapmap];0.83[CHB][hapmap];0.82[AFR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7182583	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7495518	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	nsv518840	chr15:78871288-78887171	Weak transcription Active TSS ZNF genes & repeats Strong transcription	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs692780	RP11-650L12.2	cis	Muscle Skeletal	GTEx
rs692780	CHRNA5	cis	Adipose Subcutaneous	GTEx
rs692780	CHRNA5	cis	Esophagus Mucosa	GTEx
rs692780	CHRNA3	cis	Muscle Skeletal	GTEx
rs692780	RP11-650L12.2	cis	Adipose Subcutaneous	GTEx
rs692780	CHRNA5	cis	Muscle Skeletal	GTEx
rs692780	CHRNA5	cis	Nerve Tibial	GTEx
rs692780	RP11-650L12.2	cis	Nerve Tibial	GTEx
rs692780	RP11-650L12.2	cis	lung	GTEx
rs692780	CHRNA5	cis	lung	GTEx

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78859200-78882400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr15:78860200-78881400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr15:78860200-78881600	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr15:78860200-78882200	Weak transcription	Hela-S3	cervix
5	chr15:78868000-78895800	Weak transcription	GM12878-XiMat	blood
6	chr15:78869600-78882000	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr15:78869800-78882200	Weak transcription	A549	lung
8	chr15:78872600-78881600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr15:78873600-78881200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links