Variant report

Variant	rs4338740
Chromosome Location	chr15:49735297-49735298
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1023683	0.80[YRI][hapmap];0.81[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs10519226	0.90[ASW][hapmap];0.82[CEU][hapmap];0.89[LWK][hapmap];0.94[MKK][hapmap];0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10519227	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]
rs11635308	0.81[LWK][hapmap];0.97[MKK][hapmap];0.80[YRI][hapmap];0.84[AFR][1000 genomes]
rs11639423	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs12591134	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12591799	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12592177	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12592277	0.93[GIH][hapmap];0.91[LWK][hapmap];1.00[MKK][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12592296	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12593068	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12594154	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12594827	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12595497	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12595701	0.91[ASN][1000 genomes]
rs12901416	0.81[TSI][hapmap]
rs12902107	0.81[TSI][hapmap]
rs12902794	0.81[TSI][hapmap]
rs1546424	0.81[TSI][hapmap]
rs17400427	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17400706	0.83[ASW][hapmap];0.91[LWK][hapmap];0.80[YRI][hapmap];0.90[AFR][1000 genomes]
rs17400916	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17477722	0.94[MKK][hapmap]
rs17477923	0.92[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.94[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17478618	0.83[ASW][hapmap];0.91[LWK][hapmap];1.00[MKK][hapmap];0.80[YRI][hapmap];0.90[AFR][1000 genomes]
rs17479003	0.94[MKK][hapmap];0.86[AFR][1000 genomes]
rs17479205	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17479289	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2413947	0.81[EUR][1000 genomes]
rs34635038	0.91[ASN][1000 genomes]
rs3809495	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4774539	0.81[TSI][hapmap]
rs61259878	0.84[AFR][1000 genomes]
rs7168316	0.91[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[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];1.00[ASN][1000 genomes]
rs7176697	1.00[CHB][hapmap]
rs73398264	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73398284	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73400205	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8034473	0.81[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 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

Variant related diseases (count:1)

Disease	PMID	Source
Thyroid volume	21565293	GWAS catalog

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4338740	SECISBP2L	cis	cerebellum	SCAN
rs4338740	FGF7	cis	Muscle Skeletal	GTEx
rs4338740	SECISBP2L	cis	parietal	SCAN
rs4338740	CASC4	cis	cerebellum	SCAN
rs4338740	TRPM7	cis	cerebellum	SCAN
rs4338740	TNFAIP8L3	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49716400-49737200	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr15:49721000-49736200	Weak transcription	Right Ventricle	heart
3	chr15:49730400-49744600	Weak transcription	NHLF	lung
4	chr15:49732000-49736600	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr15:49732000-49750200	Weak transcription	HSMM	muscle
6	chr15:49732200-49736200	Weak transcription	Ovary	ovary
7	chr15:49732200-49736200	Weak transcription	Stomach Smooth Muscle	stomach
8	chr15:49732400-49736800	Weak transcription	Fetal Stomach	stomach
9	chr15:49732400-49738200	Weak transcription	NHDF-Ad	bronchial
10	chr15:49732800-49741000	Weak transcription	Fetal Heart	heart
11	chr15:49733200-49741800	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr15:49733800-49736200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr15:49734400-49736400	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr15:49734600-49735400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr15:49734800-49736600	Weak transcription	Osteobl	bone
16	chr15:49735200-49736200	Weak transcription	Colon Smooth Muscle	Colon
17	chr15:49735200-49736200	Weak transcription	Rectal Smooth Muscle	rectum

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