Variant report

Variant	rs17477923
Chromosome Location	chr15:49711185-49711186
allele	C/T
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	CTCF	chr15:49711040-49711190	AG09319	gingival:	n/a	n/a
2	CTCF	chr15:49711100-49711250	AG09319	gingival:	n/a	n/a

Variant related genes	Relation type
FGF7	TF binding region

Extended variants
information (count: 37 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1023683	0.83[CEU][hapmap];0.80[YRI][hapmap];0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10519226	0.81[ASW][hapmap];0.85[LWK][hapmap];0.88[MKK][hapmap];0.84[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs10519227	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]
rs11635308	0.83[ASW][hapmap];0.97[MKK][hapmap];0.80[YRI][hapmap];0.84[AFR][1000 genomes]
rs11639423	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[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	0.95[GIH][hapmap];0.82[LWK][hapmap];0.94[MKK][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes];0.91[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]
rs12593119	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];0.85[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]
rs17400427	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs17400706	0.81[LWK][hapmap];0.80[YRI][hapmap];0.83[AFR][1000 genomes]
rs17400916	0.81[EUR][1000 genomes]
rs17477722	0.88[MKK][hapmap]
rs17478618	0.81[LWK][hapmap];0.94[MKK][hapmap];0.80[YRI][hapmap];0.83[AFR][1000 genomes]
rs17479003	0.89[MKK][hapmap]
rs17479205	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17479289	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34635038	0.91[ASN][1000 genomes]
rs3809495	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4338740	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]
rs61259878	0.84[AFR][1000 genomes]
rs7168316	0.83[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.88[MEX][hapmap];0.94[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7176697	1.00[CHB][hapmap]
rs73398264	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73398272	0.83[AFR][1000 genomes]
rs73398276	0.84[AFR][1000 genomes]
rs73398284	0.88[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs73400205	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs17477923	TRPM7	cis	cerebellum	SCAN
rs17477923	CASC4	cis	cerebellum	SCAN
rs17477923	SECISBP2L	cis	cerebellum	SCAN
rs17477923	FGF7	cis	Muscle Skeletal	GTEx
rs17477923	SECISBP2L	cis	parietal	SCAN
rs17477923	TNFAIP8L3	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49708200-49713400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr15:49708200-49713800	Weak transcription	Colon Smooth Muscle	Colon
3	chr15:49708400-49713800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr15:49708400-49714400	Weak transcription	HUVEC	blood vessel
5	chr15:49708600-49711200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr15:49708600-49714000	Weak transcription	Osteobl	bone
7	chr15:49709800-49713600	Weak transcription	Fetal Lung	lung
8	chr15:49709800-49715200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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