Variant report

Variant	rs7340886
Chromosome Location	chr4:101006705-101006706
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 85 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs1044044	0.80[CHB][hapmap];0.84[JPT][hapmap]
rs10516458	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs11097681	0.82[CHB][hapmap];0.83[JPT][hapmap]
rs11097687	0.92[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs11723477	0.94[ASN][1000 genomes]
rs11732182	0.94[ASN][1000 genomes]
rs11735694	0.94[ASN][1000 genomes]
rs11736218	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs11736719	0.94[ASN][1000 genomes]
rs11736750	0.82[CHB][hapmap];0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs11931053	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs11932783	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs11932845	0.94[ASN][1000 genomes]
rs11935767	0.89[ASN][1000 genomes]
rs11936580	0.80[ASN][1000 genomes]
rs11937848	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11937985	0.84[JPT][hapmap]
rs11939538	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs11940617	0.94[ASN][1000 genomes]
rs11941520	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs11942532	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11944693	0.96[ASN][1000 genomes]
rs11945303	0.84[JPT][hapmap]
rs11947412	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17029662	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs17029673	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs17029724	0.82[ASN][1000 genomes]
rs2070738	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs2081626	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs2276939	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs36109329	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4343735	0.99[ASN][1000 genomes]
rs4492010	0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs55705206	0.87[AFR][1000 genomes]
rs55888547	0.82[ASN][1000 genomes]
rs56159765	0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs56311063	0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs57253200	0.95[ASN][1000 genomes]
rs57315614	0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs58385517	1.00[ASN][1000 genomes]
rs60070547	0.82[ASN][1000 genomes]
rs60524451	0.95[ASN][1000 genomes]
rs61351569	1.00[ASN][1000 genomes]
rs62306101	0.80[ASN][1000 genomes]
rs62306122	0.87[AFR][1000 genomes]
rs6532837	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs6532839	0.82[ASN][1000 genomes]
rs6532840	0.82[ASN][1000 genomes]
rs6532841	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6532842	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66686535	0.94[ASN][1000 genomes]
rs66775689	0.94[ASN][1000 genomes]
rs66903712	1.00[ASN][1000 genomes]
rs67560461	0.94[ASN][1000 genomes]
rs67594720	0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs67973788	0.94[ASN][1000 genomes]
rs6813794	1.00[ASN][1000 genomes]
rs6816635	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs6824513	0.80[ASN][1000 genomes]
rs6825579	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6830286	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6832726	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs6834448	0.95[ASN][1000 genomes]
rs6834813	0.95[ASN][1000 genomes]
rs6836304	0.93[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs6837281	0.94[AFR][1000 genomes]
rs6839278	0.93[CHB][hapmap];0.83[JPT][hapmap];0.94[ASN][1000 genomes]
rs6842492	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6842840	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs6845556	0.84[JPT][hapmap]
rs6858035	0.95[ASN][1000 genomes]
rs72686215	0.80[ASN][1000 genomes]
rs7340772	1.00[ASN][1000 genomes]
rs7660185	0.80[ASN][1000 genomes]
rs7660479	0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7662195	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7665301	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7666156	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs7668076	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7676597	1.00[ASN][1000 genomes]
rs7687287	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9942267	0.95[ASN][1000 genomes]
rs9942269	0.95[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	nsv427689	chr4:100931741-101216531	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv830018	chr4:100977238-101027920	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7340886	RAP1GDS1	cis	parietal	SCAN
rs7340886	MAPKSP1	cis	parietal	SCAN
rs7340886	MAPKSP1	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:100997000-101009000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr4:101002800-101008000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr4:101003200-101007800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr4:101003200-101008000	Weak transcription	NHEK	skin
5	chr4:101006200-101008600	Weak transcription	Ovary	ovary
6	chr4:101006400-101006800	Enhancers	Gastric	stomach
7	chr4:101006400-101006800	Enhancers	Right Atrium	heart
8	chr4:101006600-101007400	Weak transcription	Fetal Intestine Large	intestine
9	chr4:101006600-101008200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr4:101006600-101009800	Enhancers	Placenta	Placenta

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