Variant report

Variant	rs1267658
Chromosome Location	chr15:83214154-83214155
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chr15:83214119-83214164	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:83213257..83215653-chr15:83219949..83222640,2	K562	blood:
2	chr15:83212827..83216127-chr15:83234244..83236895,3	MCF-7	breast:

Variant related genes	Relation type
RPS17L	TF binding region

Extended variants
information (count: 108 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10152286	0.93[YRI][hapmap]
rs10163167	1.00[YRI][hapmap]
rs10400906	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs10468217	0.93[ASN][1000 genomes]
rs10906984	0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs1145172	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs1145173	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs11631963	0.95[CHB][hapmap];0.87[JPT][hapmap];0.80[ASN][1000 genomes]
rs11633829	0.95[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs11635460	0.82[GIH][hapmap]
rs11635624	0.95[CHB][hapmap];0.82[CHD][hapmap];0.82[GIH][hapmap];0.87[JPT][hapmap]
rs11637433	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs11855735	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs12148332	0.90[ASN][1000 genomes]
rs12324877	0.86[YRI][hapmap]
rs12438312	0.83[ASN][1000 genomes]
rs12438371	0.82[LWK][hapmap];0.93[YRI][hapmap]
rs12441776	0.93[YRI][hapmap]
rs12442686	0.81[ASN][1000 genomes]
rs1259180	0.94[ASN][1000 genomes]
rs1259182	0.87[ASN][1000 genomes]
rs1259183	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1267657	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1267659	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1269134	0.86[ASN][1000 genomes]
rs12916980	1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs1313492	0.89[ASN][1000 genomes]
rs1313493	0.89[ASN][1000 genomes]
rs1367841	1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs1594511	1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs17158390	0.87[ASN][1000 genomes]
rs1864699	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs1877242	0.82[GIH][hapmap]
rs2099259	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs2278355	0.91[CHB][hapmap];0.91[CHD][hapmap];0.83[ASN][1000 genomes]
rs2567635	1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs2567636	1.00[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs2678445	0.90[ASN][1000 genomes]
rs2678448	0.90[ASN][1000 genomes]
rs28374463	0.84[ASN][1000 genomes]
rs28415133	0.89[ASN][1000 genomes]
rs2870965	0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs2870966	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs28808991	0.91[ASN][1000 genomes]
rs34186444	0.87[ASN][1000 genomes]
rs35934048	0.91[ASN][1000 genomes]
rs36109438	0.89[ASN][1000 genomes]
rs3970696	1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs4778686	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs4779032	0.93[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs4779039	0.95[CHB][hapmap];0.87[JPT][hapmap];0.80[ASN][1000 genomes]
rs4779041	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs4779044	1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs4779050	0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs55924160	0.87[ASN][1000 genomes]
rs57181760	0.86[ASN][1000 genomes]
rs59746564	0.83[AFR][1000 genomes]
rs6603033	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs698500	1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs7165125	0.85[ASN][1000 genomes]
rs7167880	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs7171180	1.00[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs7178350	0.84[ASN][1000 genomes]
rs7181761	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs7182320	0.82[GIH][hapmap]
rs7182403	0.86[ASN][1000 genomes]
rs7183881	0.86[ASN][1000 genomes]
rs7494860	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs7496954	0.86[ASN][1000 genomes]
rs783520	0.86[ASN][1000 genomes]
rs783521	1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs783522	0.87[ASN][1000 genomes]
rs783523	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs783525	1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs783526	1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs783527	1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs783529	1.00[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs783530	0.90[ASN][1000 genomes]
rs783531	0.94[ASN][1000 genomes]
rs783532	0.93[ASN][1000 genomes]
rs783533	0.92[ASN][1000 genomes]
rs783534	0.92[ASN][1000 genomes]
rs783535	0.89[ASN][1000 genomes]
rs783536	0.91[ASN][1000 genomes]
rs783537	0.89[ASN][1000 genomes]
rs783539	1.00[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs783540	1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs783543	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs783545	0.91[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs8023333	0.95[LWK][hapmap];0.88[MKK][hapmap];0.84[AFR][1000 genomes]
rs803687	0.95[ASN][1000 genomes]
rs803688	0.97[ASN][1000 genomes]
rs803747	1.00[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs8040293	0.84[ASN][1000 genomes]
rs8043401	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs9652567	0.94[CHB][hapmap];0.95[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427965	chr15:82741381-83310525	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	nsv428309	chr15:82741381-83310525	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	esv2758391	chr15:82879646-83310525	Bivalent Enhancer Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	esv2760046	chr15:82879646-83310525	Strong transcription Enhancers Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
5	nsv428645	chr15:83069951-83227151	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	esv10828	chr15:83096440-83219640	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	nsv1035899	chr15:83108446-83315731	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
8	nsv833071	chr15:83123646-83310510	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
9	esv3444210	chr15:83169297-83214995	Weak transcription Strong transcription	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
10	esv3312436	chr15:83169797-83214445	Weak transcription Strong transcription	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
11	esv3312437	chr15:83169797-83214445	Weak transcription Strong transcription	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
12	esv3384594	chr15:83177247-83214845	Weak transcription Strong transcription	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1267658	FAM154B	cis	lymphoblastoid	seeQTL
rs1267658	FAM154B	cis	cerebellum	SCAN
rs1267658	FAM154B	cis	parietal	SCAN
rs1267658	CPEB1	cis	parietal	SCAN
rs1267658	RASGRF1	cis	cerebellum	SCAN
rs1267658	LOC283726	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:83212600-83214200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr15:83212600-83214200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr15:83212600-83214200	Weak transcription	Brain Hippocampus Middle	brain
4	chr15:83212600-83214200	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr15:83212600-83214200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr15:83212600-83214200	Weak transcription	K562	blood
7	chr15:83213000-83215400	Weak transcription	Brain Substantia Nigra	brain
8	chr15:83213000-83217200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr15:83213200-83217400	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr15:83213200-83220600	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr15:83213600-83218600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr15:83213800-83217400	Weak transcription	Aorta	Aorta
13	chr15:83214000-83216200	Strong transcription	Brain Angular Gyrus	brain
14	chr15:83214000-83216200	Strong transcription	Brain Anterior Caudate	brain
15	chr15:83214000-83216200	Strong transcription	Brain Cingulate Gyrus	brain
16	chr15:83214000-83217200	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr15:83214000-83217200	Weak transcription	Fetal Lung	lung
18	chr15:83214000-83224800	Strong transcription	Stomach Smooth Muscle	stomach

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