Variant report

Variant	rs10015883
Chromosome Location	chr4:120268146-120268147
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 96 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10000544	0.84[ASN][1000 genomes]
rs10002914	0.83[ASN][1000 genomes]
rs10003742	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10004114	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10006192	0.83[ASN][1000 genomes]
rs10012408	0.86[ASN][1000 genomes]
rs10013652	0.83[ASN][1000 genomes]
rs10016241	0.86[ASN][1000 genomes]
rs10021601	0.83[ASN][1000 genomes]
rs10022448	0.86[ASN][1000 genomes]
rs10025925	0.85[ASN][1000 genomes]
rs10028773	0.86[ASN][1000 genomes]
rs10517834	0.82[ASN][1000 genomes]
rs10518300	0.81[CHD][hapmap]
rs10518329	0.83[CHB][hapmap];0.86[CHD][hapmap]
rs11098505	0.83[ASN][1000 genomes]
rs11098506	0.87[CHB][hapmap];0.82[ASN][1000 genomes]
rs1155577	0.85[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.83[GIH][hapmap];0.89[TSI][hapmap]
rs11723550	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11724758	1.00[ASW][hapmap];0.92[CEU][hapmap];0.80[CHD][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs11731571	0.81[CHD][hapmap]
rs11732621	0.80[TSI][hapmap]
rs12374244	0.81[ASN][1000 genomes]
rs12374245	0.81[ASN][1000 genomes]
rs12374352	0.81[ASN][1000 genomes]
rs12499602	0.83[ASN][1000 genomes]
rs12501602	0.81[ASN][1000 genomes]
rs12502393	0.82[ASN][1000 genomes]
rs12502524	0.84[ASN][1000 genomes]
rs12506445	0.81[ASN][1000 genomes]
rs12506487	0.84[ASN][1000 genomes]
rs12510133	0.84[ASN][1000 genomes]
rs12510451	0.83[ASN][1000 genomes]
rs12510487	0.81[ASN][1000 genomes]
rs12513310	0.80[ASN][1000 genomes]
rs12711071	0.80[CHD][hapmap]
rs13104219	0.87[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap]
rs13104572	0.81[ASN][1000 genomes]
rs13105020	0.81[ASN][1000 genomes]
rs13125526	0.82[ASN][1000 genomes]
rs13132082	0.83[ASN][1000 genomes]
rs13134517	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs13139045	0.91[CHD][hapmap]
rs1480933	0.84[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.83[GIH][hapmap];0.91[TSI][hapmap]
rs1511025	0.81[CHD][hapmap]
rs1814815	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1980025	0.80[CHD][hapmap]
rs2017058	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2036858	0.87[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs2136911	0.86[ASN][1000 genomes]
rs28369518	0.84[ASN][1000 genomes]
rs28396837	0.84[ASN][1000 genomes]
rs28437684	0.85[ASN][1000 genomes]
rs28439855	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28501434	0.83[ASN][1000 genomes]
rs28599836	0.86[ASN][1000 genomes]
rs28668103	0.83[ASN][1000 genomes]
rs28691602	0.84[ASN][1000 genomes]
rs28714087	0.86[ASN][1000 genomes]
rs28726222	0.83[ASN][1000 genomes]
rs3864142	0.81[ASN][1000 genomes]
rs3864144	0.84[ASN][1000 genomes]
rs4643791	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55820750	0.84[ASN][1000 genomes]
rs6815291	0.84[ASN][1000 genomes]
rs6824111	0.87[CHB][hapmap];0.83[ASN][1000 genomes]
rs6824169	0.83[ASN][1000 genomes]
rs6838009	0.86[ASN][1000 genomes]
rs6843229	0.96[CEU][hapmap];0.85[CHB][hapmap];0.85[GIH][hapmap];0.82[JPT][hapmap];0.81[MEX][hapmap];0.91[TSI][hapmap]
rs6843509	0.80[TSI][hapmap]
rs6844263	0.81[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs6846966	0.81[ASN][1000 genomes]
rs6847586	0.82[ASN][1000 genomes]
rs6847778	0.83[ASN][1000 genomes]
rs6857892	0.83[ASN][1000 genomes]
rs7665125	0.83[CHB][hapmap]
rs7672594	0.81[CHD][hapmap]
rs7677068	0.83[ASN][1000 genomes]
rs878372	0.81[CHD][hapmap]
rs9637624	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9799664	0.82[ASN][1000 genomes]
rs9991221	0.83[ASN][1000 genomes]
rs9991959	0.81[CHD][hapmap]
rs9995136	0.87[CHB][hapmap];0.82[ASN][1000 genomes]
rs9995716	0.85[ASN][1000 genomes]
rs9996586	0.81[ASN][1000 genomes]
rs9999724	0.80[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916641	chr4:119780023-120777320	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv1012868	chr4:120014630-120464880	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv537232	chr4:120014630-120464880	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
4	nsv428769	chr4:120205572-120363323	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv879841	chr4:120244085-120388406	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv879842	chr4:120244085-120424087	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv427694	chr4:120250511-120501728	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	esv2538163	chr4:120252854-120388678	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	nsv964091	chr4:120255342-120290951	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10015883	FLJ14186///LOC284701///LOC441124///LOC728624	Cis_1M	lymphoblastoid	RTeQTL
rs10015883	BBS7	cis	cerebellum	SCAN
rs10015883	TRPC3	cis	parietal	SCAN
rs10015883	USP53	cis	parietal	SCAN
rs10015883	LOC645513	Cis_1M	lymphoblastoid	RTeQTL
rs10015883	SYNPO2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120266400-120275000	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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