Variant report

Variant	rs13083654
Chromosome Location	chr3:23286684-23286685
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:23284952..23287695-chr3:23289326..23291059,2	K562	blood:

Extended variants
information (count: 93 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10510537	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs13059557	0.84[AMR][1000 genomes]
rs13060112	1.00[MKK][hapmap];0.84[TSI][hapmap]
rs13060251	1.00[YRI][hapmap]
rs13063183	0.87[AMR][1000 genomes]
rs13063185	1.00[YRI][hapmap]
rs13063451	1.00[YRI][hapmap]
rs13063986	1.00[CEU][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes]
rs13066741	1.00[YRI][hapmap]
rs13067514	1.00[YRI][hapmap]
rs13070865	0.87[AMR][1000 genomes]
rs13076527	0.88[LWK][hapmap];1.00[YRI][hapmap]
rs13077333	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13084250	0.81[EUR][1000 genomes]
rs13084327	1.00[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes]
rs13087234	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13087563	1.00[YRI][hapmap]
rs13089963	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13090303	1.00[CEU][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes]
rs13090335	1.00[YRI][hapmap]
rs13092830	1.00[YRI][hapmap]
rs13095736	1.00[CEU][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes]
rs13095887	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13095960	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13096187	0.83[CEU][hapmap]
rs13098494	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[CHD][hapmap];0.85[JPT][hapmap];0.87[LWK][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes]
rs1495132	0.95[ASN][1000 genomes]
rs17012823	0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs17012834	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs17012844	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs17012852	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs17012861	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17012897	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17012927	0.86[CHB][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs17012943	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs17012959	0.86[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs17012969	0.86[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs17012988	0.86[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs17012998	0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs17013003	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs17013023	0.86[ASN][1000 genomes]
rs17013026	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs17013029	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs17013035	0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs17013049	0.86[ASN][1000 genomes]
rs17013104	0.88[JPT][hapmap]
rs17013116	0.88[JPT][hapmap]
rs17013125	0.88[JPT][hapmap]
rs17013128	0.88[JPT][hapmap]
rs17013152	0.94[CHD][hapmap];0.88[JPT][hapmap]
rs17013216	0.88[JPT][hapmap]
rs17013219	0.86[JPT][hapmap]
rs17013223	0.94[CHD][hapmap];0.88[JPT][hapmap]
rs17013241	1.00[CEU][hapmap];0.88[JPT][hapmap]
rs17345745	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHD][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes]
rs17404982	0.87[AMR][1000 genomes]
rs2014132	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2291720	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs34108997	0.92[AMR][1000 genomes]
rs34239585	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34259979	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34513914	0.81[EUR][1000 genomes]
rs34646795	0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34928302	0.87[AMR][1000 genomes]
rs34972244	0.84[AMR][1000 genomes]
rs35024744	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35038414	0.87[AMR][1000 genomes]
rs35059447	0.87[AMR][1000 genomes]
rs35098118	0.87[AMR][1000 genomes]
rs35236373	0.87[AMR][1000 genomes]
rs35320722	0.87[AMR][1000 genomes]
rs35743404	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36004369	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs36123653	0.80[AMR][1000 genomes]
rs61707213	0.87[AMR][1000 genomes]
rs71322175	0.84[AMR][1000 genomes]
rs71322180	0.87[AMR][1000 genomes]
rs71322181	0.87[AMR][1000 genomes]
rs71322186	0.84[AMR][1000 genomes]
rs73044329	0.81[ASN][1000 genomes]
rs73044337	0.81[ASN][1000 genomes]
rs73044339	0.81[ASN][1000 genomes]
rs73050236	0.81[ASN][1000 genomes]
rs73050238	0.81[ASN][1000 genomes]
rs73050257	0.85[ASN][1000 genomes]
rs73050270	0.85[ASN][1000 genomes]
rs73050276	0.85[ASN][1000 genomes]
rs9857217	1.00[CEU][hapmap];0.82[AMR][1000 genomes]
rs9873329	0.92[CEU][hapmap];0.94[CHD][hapmap];0.88[JPT][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.80[AMR][1000 genomes]

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	nsv834636	chr3:23138653-23301443	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1014701	chr3:23257658-23416094	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv589947	chr3:23277838-23403943	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv1002823	chr3:23277838-23623083	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13083654	THRB	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23274800-23298200	Weak transcription	Aorta	Aorta
2	chr3:23278600-23289600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr3:23280200-23291400	Weak transcription	Psoas Muscle	Psoas
4	chr3:23280400-23290600	Weak transcription	Primary B cells from peripheral blood	blood
5	chr3:23281400-23298200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr3:23282000-23290200	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr3:23282200-23289000	Weak transcription	Adipose Nuclei	Adipose
8	chr3:23282200-23294600	Weak transcription	A549	lung
9	chr3:23283000-23286800	Enhancers	Brain Hippocampus Middle	brain
10	chr3:23283200-23296000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr3:23283600-23302200	Weak transcription	Left Ventricle	heart
12	chr3:23283800-23292000	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr3:23284800-23286800	Enhancers	Brain Anterior Caudate	brain
14	chr3:23285000-23290000	Weak transcription	Brain Cingulate Gyrus	brain
15	chr3:23285000-23292400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr3:23286400-23289600	Weak transcription	Brain Angular Gyrus	brain
17	chr3:23286600-23289000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr3:23286600-23289600	Weak transcription	Brain Substantia Nigra	brain

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