Variant report

Variant	rs11188929
Chromosome Location	chr10:98573366-98573367
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 79 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10437452	1.00[ASN][1000 genomes]
rs11188937	1.00[CEU][hapmap];0.83[GIH][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap];0.80[EUR][1000 genomes]
rs11188939	1.00[CEU][hapmap]
rs11188940	0.80[EUR][1000 genomes]
rs11188947	0.80[EUR][1000 genomes]
rs11188954	1.00[CEU][hapmap];0.85[TSI][hapmap]
rs11188956	0.80[ASW][hapmap];0.83[GIH][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap]
rs11188959	0.80[ASW][hapmap];1.00[CEU][hapmap];0.83[GIH][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap]
rs11188978	1.00[ASN][1000 genomes]
rs12240946	1.00[ASN][1000 genomes]
rs12241405	1.00[ASN][1000 genomes]
rs12241564	1.00[ASN][1000 genomes]
rs12242330	1.00[CEU][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap]
rs12243114	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12243551	0.93[ASW][hapmap];1.00[CEU][hapmap];0.83[GIH][hapmap];0.83[LWK][hapmap];0.86[MEX][hapmap];0.89[MKK][hapmap];0.92[TSI][hapmap]
rs12244490	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12246067	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs12248349	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12249381	0.93[ASW][hapmap];0.83[GIH][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap]
rs12249891	0.80[EUR][1000 genomes]
rs12250548	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12252435	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs12254525	1.00[ASN][1000 genomes]
rs12256424	0.80[EUR][1000 genomes]
rs12258355	1.00[CEU][hapmap];0.85[TSI][hapmap]
rs12259265	0.80[EUR][1000 genomes]
rs12261278	0.80[EUR][1000 genomes]
rs12261881	0.80[EUR][1000 genomes]
rs12262784	0.86[ASW][hapmap];1.00[CEU][hapmap];0.83[GIH][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap];0.80[EUR][1000 genomes]
rs12264014	0.89[AFR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12264950	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12265242	0.86[ASW][hapmap];0.83[GIH][hapmap];0.85[TSI][hapmap]
rs12265606	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12266068	0.80[EUR][1000 genomes]
rs12266185	0.80[EUR][1000 genomes]
rs12267926	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs12268216	0.86[ASW][hapmap];1.00[CEU][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap]
rs12268272	0.86[ASW][hapmap];0.86[MEX][hapmap]
rs17112175	0.93[ASW][hapmap];1.00[CEU][hapmap];0.83[GIH][hapmap];0.83[LWK][hapmap];0.86[MEX][hapmap];0.89[MKK][hapmap];0.92[TSI][hapmap]
rs17112190	0.80[ASW][hapmap];1.00[CEU][hapmap];0.83[GIH][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap]
rs2104785	0.80[EUR][1000 genomes]
rs2183449	1.00[ASN][1000 genomes]
rs28505353	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4394767	1.00[CEU][hapmap]
rs57262746	0.82[EUR][1000 genomes]
rs57501540	1.00[ASN][1000 genomes]
rs57716318	0.80[EUR][1000 genomes]
rs58270704	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58409956	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6584101	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7071211	0.86[ASW][hapmap];0.83[GIH][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap];1.00[ASN][1000 genomes]
rs7072273	0.80[ASW][hapmap];0.83[GIH][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap]
rs7073150	1.00[ASN][1000 genomes]
rs7081197	1.00[ASN][1000 genomes]
rs7082838	0.93[ASW][hapmap];0.83[GIH][hapmap];0.83[LWK][hapmap];0.86[MEX][hapmap];0.89[MKK][hapmap];0.92[TSI][hapmap];1.00[ASN][1000 genomes]
rs7085822	0.86[ASW][hapmap];1.00[CEU][hapmap];0.83[GIH][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap]
rs7086875	1.00[ASN][1000 genomes]
rs7090441	1.00[ASN][1000 genomes]
rs7090690	1.00[ASN][1000 genomes]
rs7090880	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73318637	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73318641	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73320607	1.00[ASN][1000 genomes]
rs74153734	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7893325	1.00[ASN][1000 genomes]
rs7894138	1.00[ASN][1000 genomes]
rs7894418	0.80[EUR][1000 genomes]
rs7895914	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7906294	1.00[ASN][1000 genomes]
rs7910221	0.80[ASW][hapmap];1.00[CEU][hapmap];0.86[MEX][hapmap];0.80[EUR][1000 genomes]
rs7918085	0.86[ASW][hapmap];1.00[CEU][hapmap];0.83[GIH][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap];0.80[EUR][1000 genomes]
rs7920238	1.00[ASN][1000 genomes]
rs7921193	0.80[EUR][1000 genomes]
rs7921216	0.80[EUR][1000 genomes]
rs7921885	0.86[ASW][hapmap];1.00[CEU][hapmap];0.83[GIH][hapmap];0.85[TSI][hapmap]

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	nsv532232	chr10:98360775-99141797	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv895910	chr10:98386483-98640994	ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
3	nsv1053801	chr10:98506832-98610101	Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
4	nsv825532	chr10:98567434-98618034	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11188929	BLOC1S2	cis	parietal	SCAN
rs11188929	CWF19L1	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:98563400-98576800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr10:98572400-98574200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr10:98573200-98573400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr10:98573200-98574800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr10:98573200-98574800	Enhancers	HSMM	muscle

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