Variant report

Variant	rs9642841
Chromosome Location	chr8:119445360-119445361
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 109 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs10094604	0.84[ASN][1000 genomes]
rs10096317	0.95[CHB][hapmap];0.98[CHD][hapmap];0.84[GIH][hapmap];0.85[ASN][1000 genomes]
rs10101386	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10108907	0.88[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10109048	0.85[ASN][1000 genomes]
rs10282819	0.94[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10283133	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10955877	0.95[CHB][hapmap];0.82[JPT][hapmap]
rs10955878	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10955879	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10955881	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs10955883	0.95[CHB][hapmap];0.87[ASN][1000 genomes]
rs10955884	0.95[CHB][hapmap];0.83[GIH][hapmap];0.87[ASN][1000 genomes]
rs10955885	0.95[CHB][hapmap];0.98[CHD][hapmap];0.84[GIH][hapmap];0.88[ASN][1000 genomes]
rs10955886	0.88[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10955887	0.95[CHB][hapmap];0.98[CHD][hapmap];0.84[GIH][hapmap];0.81[LWK][hapmap];0.85[ASN][1000 genomes]
rs11773916	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11773953	0.84[ASN][1000 genomes]
rs11777111	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11782499	0.88[ASN][1000 genomes]
rs11784091	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11784138	0.83[ASN][1000 genomes]
rs11991196	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11994945	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12155913	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12156188	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12156430	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12544750	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12675551	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.89[ASN][1000 genomes]
rs12677506	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12678159	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs12679343	0.94[CHB][hapmap];0.85[ASN][1000 genomes]
rs12679866	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12679873	0.95[CHB][hapmap];0.87[JPT][hapmap];0.80[ASN][1000 genomes]
rs12681581	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.89[ASN][1000 genomes]
rs12681600	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs13248112	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13251051	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13251354	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13251719	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13253470	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13253764	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13255144	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13260753	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13263320	1.00[CHB][hapmap];0.98[CHD][hapmap];0.89[ASN][1000 genomes]
rs13265657	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs13269591	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs34696908	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4075614	0.95[CHB][hapmap];0.98[CHD][hapmap];0.84[GIH][hapmap];0.84[ASN][1000 genomes]
rs4128894	0.95[CHB][hapmap];0.88[ASN][1000 genomes]
rs4242578	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4242579	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4242580	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs4375037	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4443692	0.88[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4492409	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4493938	0.91[CHB][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4548208	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4601348	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4626637	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4629902	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4631494	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4876416	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4876417	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4876832	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4876833	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4876835	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4876836	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4876837	0.95[CHB][hapmap];0.87[ASN][1000 genomes]
rs4876838	0.95[CHB][hapmap];0.88[ASN][1000 genomes]
rs4876839	0.95[CHB][hapmap];0.98[CHD][hapmap];0.84[GIH][hapmap];0.81[LWK][hapmap];0.85[ASN][1000 genomes]
rs4876840	0.88[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4876841	0.95[CHB][hapmap];0.98[CHD][hapmap];0.84[GIH][hapmap];0.81[LWK][hapmap];0.85[ASN][1000 genomes]
rs4876842	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4876845	0.88[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59298785	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61636365	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62533427	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6469747	0.88[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6981538	0.91[CHB][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6982369	0.88[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6983068	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6985503	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7012582	0.91[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7812733	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7812880	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7813395	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7825963	0.88[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7826257	0.88[CEU][hapmap];0.90[CHB][hapmap];0.82[JPT][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7826375	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7826888	0.83[ASN][1000 genomes]
rs7830347	0.88[ASN][1000 genomes]
rs7830423	0.95[CHB][hapmap];0.98[CHD][hapmap];0.81[LWK][hapmap];0.83[ASN][1000 genomes]
rs7831361	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7831501	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7835295	0.88[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7838464	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7846218	0.91[CHB][hapmap];0.86[JPT][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9297587	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.89[ASN][1000 genomes]
rs9643128	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9643129	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9643130	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9656927	0.95[CHB][hapmap];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv612047	chr8:118939094-119468609	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1032681	chr8:119153316-119609948	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv539737	chr8:119153316-119609948	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv1016379	chr8:119164234-119448910	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv831443	chr8:119390590-119590662	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
6	esv20481	chr8:119445015-119446781	Enhancers Weak transcription ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9642841	TRPS1	cis	cerebellum	SCAN
rs9642841	MED30	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:119434800-119451800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr8:119438000-119446400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr8:119442200-119449200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr8:119443800-119445400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr8:119445000-119445600	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr8:119445200-119445400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr8:119445200-119445600	Weak transcription	Aorta	Aorta
8	chr8:119445200-119445600	Enhancers	HUVEC	blood vessel
9	chr8:119445200-119445800	Enhancers	NHLF	lung
10	chr8:119445200-119446000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr8:119445200-119446000	Enhancers	NHDF-Ad	bronchial
12	chr8:119445200-119446200	Enhancers	Osteobl	bone
13	chr8:119445200-119446800	Enhancers	iPS-18 Cell Line	embryonic stem cell

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