Variant report

Variant	rs10272997
Chromosome Location	chr7:70764516-70764517
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10226199	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10231965	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10256635	0.94[CEU][hapmap];0.90[JPT][hapmap];0.90[EUR][1000 genomes]
rs10261998	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10263619	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10266560	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11976781	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12155368	0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs12668780	1.00[CEU][hapmap];0.88[JPT][hapmap]
rs12669285	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12673556	0.81[CEU][hapmap];0.85[JPT][hapmap]
rs1465231	0.88[CHD][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs1558003	0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs1574440	0.94[CEU][hapmap];0.85[JPT][hapmap]
rs1922527	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2141885	0.81[CEU][hapmap];0.85[JPT][hapmap]
rs2527289	0.81[CEU][hapmap];0.85[JPT][hapmap]
rs2527297	0.80[CEU][hapmap];0.84[JPT][hapmap]
rs2527298	0.81[CEU][hapmap];0.85[JPT][hapmap]
rs2527312	0.80[CEU][hapmap];0.85[JPT][hapmap]
rs28631036	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28670821	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2867411	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28799658	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3923571	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4073529	0.93[CEU][hapmap];0.89[JPT][hapmap]
rs4446620	0.92[CHD][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs6460649	0.91[EUR][1000 genomes]
rs67615560	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6942815	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6943983	0.86[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6961808	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6976562	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6976574	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6976591	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73177835	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73179792	0.88[EUR][1000 genomes]
rs73356099	0.86[EUR][1000 genomes]
rs7778324	0.81[CEU][hapmap];0.85[JPT][hapmap]
rs7792223	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9638618	0.85[GIH][hapmap]
rs9690269	0.85[ASN][1000 genomes]
rs9886302	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[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	nsv519090	chr7:70085934-71071896	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
2	nsv1015261	chr7:70404302-71255933	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10272997	STAG3L4	cis	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:70751200-70768200	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr7:70751800-70768600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr7:70751800-70768800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr7:70752200-70773000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr7:70756000-70765000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr7:70756000-70765200	Weak transcription	Fetal Heart	heart
7	chr7:70758800-70765200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr7:70760400-70765200	Weak transcription	Ovary	ovary
9	chr7:70760400-70765400	Weak transcription	Fetal Stomach	stomach
10	chr7:70764000-70768800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr7:70764200-70765000	Weak transcription	Fetal Muscle Trunk	muscle
12	chr7:70764200-70765000	Weak transcription	Fetal Muscle Leg	muscle
13	chr7:70764200-70765600	Weak transcription	Colon Smooth Muscle	Colon

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