Variant report

Variant	rs11159388
Chromosome Location	chr14:79417714-79417715
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10873319	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap]
rs11159385	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11159386	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11159387	1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs11159389	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11159390	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11845894	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11847534	0.81[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11847702	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11849555	1.00[MEX][hapmap]
rs12050287	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12588364	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap]
rs149088	0.82[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs150774	0.89[JPT][hapmap]
rs154323	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs154329	0.82[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs154330	0.82[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs154333	0.82[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs154334	0.87[ASN][1000 genomes]
rs154336	0.87[ASN][1000 genomes]
rs154340	0.82[CHB][hapmap];0.89[JPT][hapmap]
rs154343	0.87[CHB][hapmap];0.87[CHD][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs154376	0.82[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap]
rs154378	0.82[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap]
rs17108397	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs17108401	0.91[ASN][1000 genomes]
rs17108405	1.00[ASW][hapmap];0.87[CHB][hapmap];0.85[CHD][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];0.86[MKK][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs17108413	0.91[ASN][1000 genomes]
rs17108429	0.91[CHB][hapmap];0.88[CHD][hapmap];0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs220103	0.86[ASN][1000 genomes]
rs220104	0.82[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs2270963	0.91[CHB][hapmap]
rs2272292	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2272293	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs31349	0.82[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs31351	0.84[ASN][1000 genomes]
rs31352	0.84[ASN][1000 genomes]
rs31414	0.86[CHB][hapmap]
rs31415	0.91[CHB][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs31417	0.91[CHB][hapmap];0.88[CHD][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs31419	0.82[ASN][1000 genomes]
rs31420	0.91[CHB][hapmap];0.91[CHD][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs31421	0.91[CHB][hapmap];0.89[JPT][hapmap]
rs31422	0.91[CHB][hapmap];0.89[JPT][hapmap]
rs31424	0.84[JPT][hapmap]
rs31426	0.85[CHD][hapmap]
rs31436	0.87[CHB][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs31437	0.87[CHB][hapmap];0.85[CHD][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs31439	0.99[ASN][1000 genomes]
rs31441	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs31448	0.87[CHB][hapmap];0.85[CHD][hapmap];0.89[JPT][hapmap]
rs31450	0.82[CHB][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs3817535	0.92[ASN][1000 genomes]
rs60746359	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61330422	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61995265	0.83[ASN][1000 genomes]
rs7142134	0.81[ASW][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap]
rs7144101	0.93[ASW][hapmap];0.80[CHD][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap]
rs7154350	0.80[CHD][hapmap]
rs7157841	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs730024	0.82[ASN][1000 genomes]
rs8003966	0.96[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs8007461	0.81[ASW][hapmap];0.87[CHB][hapmap];0.85[CHD][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs8011529	0.82[CHB][hapmap];0.89[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832838	chr14:79306627-79445382	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
2	nsv1048274	chr14:79323592-79417906	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
3	nsv917249	chr14:79388181-79574717	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv1041991	chr14:79394408-79644886	Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv1037112	chr14:79412455-79527656	Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11159388	CD247	trans	brain	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:79416200-79417800	Enhancers	Fetal Intestine Large	intestine
2	chr14:79416400-79417800	Enhancers	HUVEC	blood vessel
3	chr14:79416600-79418000	Enhancers	Fetal Intestine Small	intestine
4	chr14:79416600-79418400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr14:79416800-79418800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr14:79416800-79426200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr14:79416800-79436000	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr14:79417400-79417800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr14:79417400-79418000	Weak transcription	HUES64 Cell Line	embryonic stem cell

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