Variant report

Variant	rs13098494
Chromosome Location	chr3:23415697-23415698
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:23413992..23416641-chr3:23420982..23423774,2	MCF-7	breast:

Extended variants
information (count: 120 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:113)

rs_ID	r²[population]
rs1007332	1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1011754	1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10510537	0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs13059557	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13060251	1.00[YRI][hapmap]
rs13063183	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13063185	1.00[YRI][hapmap]
rs13063451	1.00[YRI][hapmap]
rs13063986	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13065375	1.00[YRI][hapmap]
rs13066741	0.84[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs13067514	1.00[YRI][hapmap]
rs13070865	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13072325	1.00[YRI][hapmap]
rs13076527	0.89[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap]
rs13077333	0.87[AMR][1000 genomes]
rs13083654	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]
rs13084327	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13087234	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[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]
rs13087563	1.00[YRI][hapmap]
rs13089963	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13090303	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13090335	1.00[YRI][hapmap]
rs13092830	1.00[YRI][hapmap]
rs13095736	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13095960	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13096187	0.83[CEU][hapmap];0.87[LWK][hapmap]
rs13098798	0.82[AFR][1000 genomes]
rs1463835	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs17012834	0.85[JPT][hapmap]
rs17012844	0.85[JPT][hapmap]
rs17012852	0.85[JPT][hapmap]
rs17012861	0.85[JPT][hapmap]
rs17012897	0.87[AMR][1000 genomes]
rs17012927	0.83[ASN][1000 genomes]
rs17012943	0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs17012959	0.88[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs17012969	0.88[CHB][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs17012988	0.88[CHB][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs17012998	0.88[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs17013003	0.88[CHB][hapmap];0.85[JPT][hapmap]
rs17013023	0.88[ASN][1000 genomes]
rs17013026	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs17013029	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs17013035	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs17013049	0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs17013104	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs17013116	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs17013125	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs17013128	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs17013152	0.88[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs17013216	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs17013219	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs17013223	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs17013241	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17013245	1.00[CHB][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs17013286	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs17013314	0.89[ASN][1000 genomes]
rs17013320	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs17013322	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs17013333	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs17013344	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs17013348	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs17013383	1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs17013390	1.00[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs17013393	0.83[ASN][1000 genomes]
rs17013398	1.00[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs17013406	1.00[CHB][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs17013409	1.00[CHB][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs17013418	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs17013422	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs17013429	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs17013433	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs17345745	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17404982	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1985664	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2014132	0.85[JPT][hapmap]
rs2291720	0.85[JPT][hapmap]
rs34011881	0.89[ASN][1000 genomes]
rs34108997	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34239585	0.87[AMR][1000 genomes]
rs34646795	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34896901	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34928302	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34972244	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35024744	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35038414	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35059447	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35098118	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35156003	0.82[AFR][1000 genomes]
rs35179250	0.82[AFR][1000 genomes]
rs35236373	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35320722	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35497505	0.82[AFR][1000 genomes]
rs35743404	0.87[AMR][1000 genomes]
rs35907941	0.82[EUR][1000 genomes]
rs35975795	0.82[AFR][1000 genomes]
rs35982877	0.81[ASN][1000 genomes]
rs36004369	0.87[AMR][1000 genomes]
rs36123653	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4574222	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs57427415	0.89[ASN][1000 genomes]
rs59034251	0.80[ASN][1000 genomes]
rs61707213	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs71322175	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs71322180	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs71322181	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs71322182	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs71322186	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs71322188	0.99[EUR][1000 genomes]
rs983288	0.86[ASN][1000 genomes]
rs9857217	1.00[CEU][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9873329	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv1007373	chr3:23367952-23710331	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv876624	chr3:23385877-23483536	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv876625	chr3:23390301-23509597	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv1012236	chr3:23408427-23469063	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv1010032	chr3:23408985-23469063	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13098494	THRB	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23404200-23418000	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr3:23404400-23418000	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr3:23409200-23431800	Weak transcription	Aorta	Aorta
4	chr3:23410800-23426800	Weak transcription	Brain Cingulate Gyrus	brain
5	chr3:23415000-23416000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr3:23415000-23418000	Weak transcription	Left Ventricle	heart
7	chr3:23415000-23418000	Weak transcription	Psoas Muscle	Psoas
8	chr3:23415000-23418400	Weak transcription	Brain Substantia Nigra	brain
9	chr3:23415000-23422000	Weak transcription	Brain Hippocampus Middle	brain
10	chr3:23415400-23418400	Weak transcription	Fetal Lung	lung

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