Variant report

Variant	rs1577876
Chromosome Location	chr13:38429073-38429074
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1077026	0.87[EUR][1000 genomes]
rs12583028	0.85[CEU][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12583641	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12872351	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12874874	1.00[ASW][hapmap];0.95[CEU][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1415602	0.84[EUR][1000 genomes]
rs17272200	0.85[CEU][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1819607	0.91[MEX][hapmap]
rs2093812	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2104326	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34311615	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34824702	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35681998	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3812837	0.91[MEX][hapmap]
rs3812840	0.91[MEX][hapmap]
rs9532122	0.85[CEU][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9532125	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9532126	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9532128	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];0.83[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9532131	0.91[MEX][hapmap]
rs9548060	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9548061	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9548064	0.95[CEU][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9548065	0.94[CEU][hapmap];0.91[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9548066	0.95[CEU][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9548067	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9548069	0.95[CEU][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9548070	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9548074	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9548076	1.00[ASW][hapmap];0.95[CEU][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9548077	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9548078	0.84[ASW][hapmap];0.95[CEU][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9548079	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9548080	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9548082	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9548083	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9548088	0.85[CEU][hapmap];0.89[EUR][1000 genomes]

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	nsv915901	chr13:38199035-39032633	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv899995	chr13:38395847-38438843	Enhancers Weak transcription ZNF genes & repeats Strong transcription	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
3	esv3693142	chr13:38428276-38429697	Weak transcription	n/a	n/a	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1577876	SMAD9	cis	cerebellum	SCAN
rs1577876	KL	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:38421600-38430200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr13:38423800-38435800	Weak transcription	Osteobl	bone
3	chr13:38424000-38437000	Weak transcription	Ovary	ovary

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