Variant report

Variant	rs10519227
Chromosome Location	chr15:49746364-49746365
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1023683	0.80[YRI][hapmap]
rs10519226	0.89[LWK][hapmap];0.94[MKK][hapmap];0.89[AFR][1000 genomes]
rs11632575	0.83[EUR][1000 genomes]
rs11633282	0.82[EUR][1000 genomes]
rs11635005	0.82[ASW][hapmap]
rs11635308	0.82[ASW][hapmap];0.81[LWK][hapmap];0.97[MKK][hapmap];0.85[TSI][hapmap];0.80[YRI][hapmap];0.86[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs11635354	0.86[EUR][1000 genomes]
rs11638314	0.86[EUR][1000 genomes]
rs11638606	0.82[EUR][1000 genomes]
rs12591134	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12591799	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12592177	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12592277	0.95[GIH][hapmap];0.91[LWK][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];0.91[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12592296	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12593068	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12594154	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12594827	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12595497	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12595701	0.82[ASN][1000 genomes]
rs17396536	0.82[CEU][hapmap]
rs17396747	0.82[CEU][hapmap]
rs17397211	0.81[CEU][hapmap]
rs17400427	0.89[AFR][1000 genomes]
rs17400706	0.91[ASW][hapmap];0.82[CEU][hapmap];0.91[LWK][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap];0.80[YRI][hapmap];0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17477722	0.82[ASW][hapmap];0.94[MKK][hapmap];0.84[EUR][1000 genomes]
rs17477923	0.83[ASW][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.88[MEX][hapmap];0.94[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17478618	0.91[ASW][hapmap];0.82[CEU][hapmap];0.91[LWK][hapmap];0.83[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];0.80[YRI][hapmap];0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17479003	0.82[CEU][hapmap];0.94[MKK][hapmap];0.88[TSI][hapmap];0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17479205	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17479289	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34635038	0.82[ASN][1000 genomes]
rs3809495	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4338740	0.91[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57252806	0.82[EUR][1000 genomes]
rs59112977	0.84[EUR][1000 genomes]
rs60594237	0.80[EUR][1000 genomes]
rs61259878	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7162633	0.82[EUR][1000 genomes]
rs7168316	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.98[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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7176697	1.00[CHB][hapmap]
rs73394359	0.80[EUR][1000 genomes]
rs73396235	0.82[EUR][1000 genomes]
rs73396238	0.86[EUR][1000 genomes]
rs73398223	0.82[EUR][1000 genomes]
rs73398243	0.84[EUR][1000 genomes]
rs73398264	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73398272	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs73398276	0.86[EUR][1000 genomes]
rs73398284	0.83[AFR][1000 genomes]
rs73400205	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8027094	0.84[EUR][1000 genomes]
rs8030457	0.84[EUR][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	nsv1039368	chr15:49566094-49764066	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv833002	chr15:49621400-49781799	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv9263	chr15:49734435-49809465	Active TSS Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
4	nsv526246	chr15:49738233-49749735	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Thyroid hormone levels	23408906	GWAS catalog

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10519227	SECISBP2L	cis	cerebellum	SCAN
rs10519227	CASC4	cis	cerebellum	SCAN
rs10519227	TNFAIP8L3	cis	parietal	SCAN
rs10519227	FGF7	cis	Muscle Skeletal	GTEx
rs10519227	SECISBP2L	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49732000-49750200	Weak transcription	HSMM	muscle
2	chr15:49737000-49751200	Weak transcription	Ovary	ovary
3	chr15:49741800-49747400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr15:49742000-49752000	Weak transcription	Adipose Nuclei	Adipose
5	chr15:49742800-49748000	Weak transcription	Fetal Heart	heart
6	chr15:49742800-49750400	Weak transcription	Stomach Smooth Muscle	stomach
7	chr15:49743000-49748000	Weak transcription	Fetal Lung	lung
8	chr15:49743200-49747200	Weak transcription	Rectal Smooth Muscle	rectum
9	chr15:49743200-49748400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr15:49744400-49747200	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr15:49745000-49748200	Weak transcription	NHLF	lung
12	chr15:49745400-49746400	Strong transcription	Osteobl	bone
13	chr15:49745600-49746800	Strong transcription	NHDF-Ad	bronchial
14	chr15:49745800-49746600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr15:49745800-49747200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr15:49746200-49747200	Weak transcription	Colon Smooth Muscle	Colon
17	chr15:49746200-49747800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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