Variant report

Variant	rs3949478
Chromosome Location	chr10:97473214-97473215
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 135 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:133)

rs_ID	r²[population]
rs10159941	0.92[CHB][hapmap]
rs10509687	0.85[CHB][hapmap]
rs10736093	0.85[CHD][hapmap];0.94[JPT][hapmap]
rs10748634	0.83[ASW][hapmap];0.92[CHB][hapmap];0.91[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.86[MKK][hapmap];0.82[ASN][1000 genomes]
rs10748635	0.92[CHB][hapmap]
rs10748637	0.92[CHB][hapmap]
rs10748638	0.93[CHB][hapmap];0.94[JPT][hapmap]
rs10748642	0.85[CHD][hapmap];0.94[JPT][hapmap]
rs10748643	0.85[CHD][hapmap];0.94[JPT][hapmap]
rs10748648	0.88[JPT][hapmap]
rs10786228	0.84[CHB][hapmap];0.94[JPT][hapmap]
rs10786230	0.92[CHB][hapmap]
rs10786233	0.81[ASN][1000 genomes]
rs10786235	0.92[CHB][hapmap]
rs10786236	0.94[JPT][hapmap]
rs10882646	0.92[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs10882647	0.85[JPT][hapmap]
rs10882651	0.90[JPT][hapmap]
rs10882652	0.90[JPT][hapmap]
rs10882653	0.92[CHB][hapmap]
rs10882656	0.94[JPT][hapmap]
rs10882657	0.94[JPT][hapmap]
rs10882660	0.94[JPT][hapmap]
rs10882664	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.83[MEX][hapmap];0.83[YRI][hapmap];0.81[ASN][1000 genomes]
rs10882665	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.83[MEX][hapmap];0.83[YRI][hapmap];0.81[ASN][1000 genomes]
rs10882670	0.92[CHB][hapmap]
rs10882673	0.83[JPT][hapmap]
rs10882675	0.85[CHD][hapmap];0.89[JPT][hapmap]
rs10882676	0.83[JPT][hapmap]
rs11188414	0.84[CHB][hapmap];0.94[JPT][hapmap]
rs11188459	0.92[CHB][hapmap]
rs11188485	0.92[CHB][hapmap]
rs11188486	0.94[JPT][hapmap]
rs11188488	0.92[CHB][hapmap]
rs11188497	0.93[JPT][hapmap]
rs11188513	0.84[CHD][hapmap];0.94[JPT][hapmap]
rs11596004	0.84[CHB][hapmap];0.93[JPT][hapmap]
rs11596976	0.84[ASN][1000 genomes]
rs12244124	0.85[JPT][hapmap]
rs12244559	0.90[JPT][hapmap]
rs12262943	0.92[CHB][hapmap]
rs1342790	0.94[JPT][hapmap]
rs1342791	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.83[MEX][hapmap]
rs1418709	0.94[JPT][hapmap]
rs1573112	0.85[CHD][hapmap];0.94[JPT][hapmap]
rs17111041	0.85[CHB][hapmap]
rs1890186	0.82[ASN][1000 genomes]
rs1933165	0.94[JPT][hapmap]
rs1933166	0.92[CHB][hapmap]
rs1933169	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1953710	0.92[CHB][hapmap]
rs2051052	0.85[CHD][hapmap];0.94[JPT][hapmap]
rs2153913	0.94[JPT][hapmap]
rs2153914	0.81[CHD][hapmap];0.94[JPT][hapmap]
rs2185818	0.85[CHD][hapmap];0.83[JPT][hapmap]
rs2211002	0.89[ASW][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2225893	0.85[CHB][hapmap]
rs2226163	0.94[JPT][hapmap]
rs2275273	0.85[CHB][hapmap];0.94[JPT][hapmap]
rs2275759	0.85[CHD][hapmap];0.94[JPT][hapmap]
rs2297788	0.90[JPT][hapmap]
rs2485643	0.82[ASN][1000 genomes]
rs2861147	0.94[JPT][hapmap]
rs2861148	0.94[JPT][hapmap]
rs2861149	0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2901873	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.83[MEX][hapmap];0.83[MKK][hapmap];0.83[YRI][hapmap]
rs2986401	0.85[JPT][hapmap]
rs3176881	0.94[JPT][hapmap]
rs3176883	0.92[CHB][hapmap]
rs3176891	0.94[JPT][hapmap]
rs3181123	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.83[MEX][hapmap]
rs3181124	0.85[CHD][hapmap];0.94[JPT][hapmap]
rs3181129	0.89[JPT][hapmap]
rs3181131	0.85[CHD][hapmap];0.94[JPT][hapmap]
rs3750700	0.85[CHB][hapmap];0.94[JPT][hapmap]
rs3750701	0.85[CHB][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap]
rs3793748	0.85[CHB][hapmap]
rs3793749	0.85[JPT][hapmap]
rs3814159	0.85[CHD][hapmap];0.94[JPT][hapmap]
rs3929900	0.94[JPT][hapmap]
rs3934409	0.85[CHD][hapmap];0.94[JPT][hapmap]
rs4074424	0.94[JPT][hapmap]
rs4075310	0.94[JPT][hapmap]
rs4244319	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4290159	0.92[CHB][hapmap];0.88[JPT][hapmap]
rs4396219	0.85[CHD][hapmap];0.94[JPT][hapmap]
rs4431963	0.85[CHD][hapmap];0.94[JPT][hapmap]
rs4457685	0.92[CHB][hapmap]
rs4501930	1.00[CHB][hapmap];0.91[CHD][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4551688	0.85[CHD][hapmap];0.94[JPT][hapmap]
rs4582902	0.85[CHD][hapmap];0.94[JPT][hapmap]
rs4614366	0.90[JPT][hapmap]
rs4918950	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs4918962	0.94[JPT][hapmap]
rs4918964	1.00[CHB][hapmap]
rs496426	0.83[ASW][hapmap];0.92[CHB][hapmap];0.87[CHD][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];0.83[LWK][hapmap];0.86[MKK][hapmap]
rs497331	0.85[CHB][hapmap]
rs5014871	0.94[JPT][hapmap]
rs501819	0.85[JPT][hapmap]
rs535449	0.85[JPT][hapmap]
rs57126367	0.81[ASN][1000 genomes]
rs571505	0.85[CHB][hapmap]
rs6584022	0.94[JPT][hapmap]
rs6584023	0.94[JPT][hapmap]
rs6584026	0.92[CHB][hapmap]
rs6584027	0.85[CHD][hapmap];0.94[JPT][hapmap]
rs6584028	0.92[CHB][hapmap]
rs6584033	0.92[CHB][hapmap]
rs7067762	0.94[JPT][hapmap]
rs7069234	0.92[CHB][hapmap]
rs7071836	0.85[CHD][hapmap];0.94[JPT][hapmap]
rs7072572	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7073723	0.92[CHB][hapmap]
rs7074403	0.85[CHD][hapmap];0.94[JPT][hapmap]
rs7077566	0.94[JPT][hapmap]
rs7081414	0.92[CHB][hapmap]
rs7086986	0.94[JPT][hapmap]
rs7088584	0.85[CHD][hapmap];0.94[JPT][hapmap]
rs7094855	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7095587	0.94[JPT][hapmap]
rs7096317	0.89[JPT][hapmap]
rs7098750	0.92[CHB][hapmap]
rs7893677	0.84[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs7894648	0.90[JPT][hapmap]
rs7902190	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs7905653	0.92[CHB][hapmap]
rs7909569	0.92[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7915345	0.92[CHB][hapmap]
rs7920801	0.87[JPT][hapmap]
rs7920850	0.92[CHB][hapmap]
rs945958	0.92[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs9663413	0.85[JPT][hapmap]
rs9787589	0.81[AFR][1000 genomes];0.82[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	nsv526180	chr10:97332195-97511037	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv531923	chr10:97366055-97725757	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs3949478	ENTPD1	Cis_1M	lymphoblastoid	RTeQTL
rs3949478	ENSG00000119977	cis	multi-tissue	Pritchard
rs3949478	TCTN3	Cis_1M	lymphoblastoid	RTeQTL
rs3949478	TCTN3	cis	lymphoblastoid	seeQTL
rs3949478	ALDH18A1	cis	cerebellum	SCAN
rs3949478	ENTPD1	cis	lymphoblastoid	seeQTL
rs3949478	ENTPD1	cis	Lymphoblastoid	GTEx

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:97458800-97481400	Weak transcription	Primary B cells from cord blood	blood
2	chr10:97469400-97475600	Weak transcription	Primary monocytes fromperipheralblood	blood
3	chr10:97470000-97476200	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr10:97471800-97480000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr10:97472600-97476400	Weak transcription	Placenta	Placenta
6	chr10:97473200-97473400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr10:97473200-97473600	Enhancers	Primary B cells from peripheral blood	blood

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