Variant report

Variant	rs7139348
Chromosome Location	chr12:48837020-48837021
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1807757	0.92[CEU][hapmap];0.82[TSI][hapmap]
rs2252234	0.82[AFR][1000 genomes]
rs2468939	0.82[AFR][1000 genomes]
rs2705124	0.90[CHB][hapmap];0.81[CHD][hapmap];0.86[GIH][hapmap];0.86[LWK][hapmap]
rs2705125	0.89[CHB][hapmap]
rs2705127	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2705130	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2731063	0.90[CHB][hapmap];0.81[CHD][hapmap];0.86[GIH][hapmap]
rs2731091	0.84[CEU][hapmap];0.81[TSI][hapmap]
rs2731092	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.94[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2731094	0.84[CEU][hapmap];0.81[TSI][hapmap]
rs2731096	0.90[CHB][hapmap];0.81[CHD][hapmap];0.86[GIH][hapmap];0.84[LWK][hapmap];0.83[MKK][hapmap];0.81[YRI][hapmap]
rs2731099	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2731100	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2731102	0.84[CEU][hapmap]
rs2731103	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2731105	0.90[CHB][hapmap];0.86[GIH][hapmap];0.86[LWK][hapmap]
rs2731106	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2731108	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2732447	0.83[AFR][1000 genomes]
rs2956467	0.84[CEU][hapmap]
rs4369449	0.80[CHB][hapmap]
rs4492859	0.83[GIH][hapmap]
rs7294585	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7309958	0.90[CHB][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427911	chr12:48670336-48979396	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	nsv832402	chr12:48686761-48851020	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7139348	RPAP3	cis	cerebellum	SCAN
rs7139348	C12orf54	cis	multi-tissue	Pritchard
rs7139348	KCNH3	cis	cerebellum	SCAN
rs7139348	C12orf54	cis	lymphoblastoid	seeQTL
rs7139348	C12orf54	cis	Esophagus Mucosa	GTEx

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48833800-48840400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
2	chr12:48834200-48840400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:48834200-48840400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr12:48834600-48837800	Enhancers	Hela-S3	cervix
5	chr12:48835400-48838600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr12:48835800-48837200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr12:48836400-48839600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr12:48836600-48839600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr12:48836600-48839600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr12:48836800-48839800	Weak transcription	HUES64 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links