Variant report

Variant	rs9875617
Chromosome Location	chr3:49634696-49634697
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 111 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs10212296	0.87[EUR][1000 genomes]
rs1050088	0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs1060962	0.85[GIH][hapmap]
rs10640	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs10865955	0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs11130192	1.00[JPT][hapmap]
rs11130199	0.93[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs11130203	0.90[EUR][1000 genomes]
rs11130213	0.85[ASW][hapmap];1.00[CEU][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes]
rs1131095	0.85[ASW][hapmap];1.00[CEU][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes]
rs11706370	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap]
rs11708955	0.81[EUR][1000 genomes]
rs11709525	1.00[CEU][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];0.89[LWK][hapmap];0.94[MEX][hapmap];0.81[MKK][hapmap];0.87[TSI][hapmap];0.80[AMR][1000 genomes]
rs11710037	0.86[AMR][1000 genomes]
rs11711485	0.93[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs11712569	0.85[EUR][1000 genomes]
rs11713474	0.91[EUR][1000 genomes]
rs11715915	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.91[YRI][hapmap]
rs11718165	1.00[CEU][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes]
rs11719996	0.86[EUR][1000 genomes]
rs11720264	1.00[JPT][hapmap]
rs11720597	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11917431	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11919311	0.88[GIH][hapmap];0.86[JPT][hapmap]
rs11921590	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11922013	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs11926781	0.92[EUR][1000 genomes]
rs12330269	0.87[EUR][1000 genomes]
rs12489092	1.00[JPT][hapmap]
rs12636099	0.88[ASN][1000 genomes]
rs13062429	0.83[EUR][1000 genomes]
rs13064576	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13079082	0.92[EUR][1000 genomes]
rs13085791	1.00[CEU][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes]
rs13316695	0.83[AMR][1000 genomes]
rs1464566	0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs1464567	0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs1464568	0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs1568661	0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs1801143	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.94[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.92[EUR][1000 genomes]
rs1873625	1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes]
rs1873626	0.86[JPT][hapmap]
rs2131104	0.85[GIH][hapmap]
rs2131109	0.85[GIH][hapmap]
rs2172252	1.00[CEU][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes]
rs2329020	0.85[GIH][hapmap];0.86[JPT][hapmap]
rs3197999	0.95[CEU][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.80[AMR][1000 genomes]
rs34196454	0.88[EUR][1000 genomes]
rs34293138	0.92[EUR][1000 genomes]
rs34363169	0.87[EUR][1000 genomes]
rs34427167	0.92[EUR][1000 genomes]
rs34762726	1.00[CEU][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.89[LWK][hapmap];0.94[MEX][hapmap];0.80[MKK][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes]
rs35261698	0.87[EUR][1000 genomes]
rs35701831	0.86[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs35999162	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3811697	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.89[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.92[EUR][1000 genomes]
rs3870338	0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs3924462	0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs3926569	0.89[EUR][1000 genomes]
rs4283605	1.00[CEU][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.89[LWK][hapmap];0.94[MEX][hapmap];0.80[MKK][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes]
rs4625	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.94[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.91[EUR][1000 genomes]
rs4855839	0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs4855852	0.88[GIH][hapmap];0.86[JPT][hapmap]
rs4855859	0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs4855864	0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs4855873	0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs4855877	1.00[JPT][hapmap]
rs4855881	0.85[GIH][hapmap];0.86[JPT][hapmap]
rs4855884	0.85[GIH][hapmap]
rs6446272	0.94[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.94[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap]
rs67216675	0.82[EUR][1000 genomes]
rs6766131	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.94[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.87[EUR][1000 genomes]
rs6766581	0.87[EUR][1000 genomes]
rs6770670	1.00[CEU][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes]
rs6779524	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.94[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap]
rs6782577	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs6784820	0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs6787417	0.80[ASN][1000 genomes]
rs6797664	0.87[EUR][1000 genomes]
rs6803222	0.85[ASW][hapmap];1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6997	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.94[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap]
rs7614725	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7622302	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.89[EUR][1000 genomes]
rs7630869	0.86[EUR][1000 genomes]
rs7633271	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[EUR][1000 genomes]
rs7637999	0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs7646366	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs885592	0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs9811982	1.00[CEU][hapmap]
rs9812791	1.00[CEU][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.89[LWK][hapmap];0.94[MEX][hapmap];0.80[MKK][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes]
rs9814873	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.91[YRI][hapmap]
rs9818590	0.87[EUR][1000 genomes]
rs9821311	0.89[EUR][1000 genomes]
rs9822268	1.00[CEU][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.88[LWK][hapmap];0.88[MEX][hapmap];0.80[MKK][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes]
rs9823546	1.00[CEU][hapmap];0.82[AMR][1000 genomes]
rs9824092	0.85[AMR][1000 genomes]
rs9827021	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.87[EUR][1000 genomes]
rs9827708	1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.89[LWK][hapmap];0.94[MEX][hapmap];0.80[MKK][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9833611	0.85[AMR][1000 genomes]
rs9837027	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.94[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9837341	1.00[CEU][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9841110	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.82[EUR][1000 genomes]
rs9850072	0.87[EUR][1000 genomes]
rs9853683	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes]
rs9858213	0.89[CEU][hapmap];0.81[GIH][hapmap];0.94[MEX][hapmap]
rs9858280	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.94[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9858418	0.85[EUR][1000 genomes]
rs9858542	1.00[CEU][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes]
rs9862080	0.85[AMR][1000 genomes]
rs9882740	1.00[CEU][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.81[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv508217	chr3:49615446-49769896	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer 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	55 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs9875617	GPX1	cis	parietal	SCAN
rs9875617	ZNF589	cis	parietal	SCAN
rs9875617	IHPK2	Cis_1M	lymphoblastoid	RTeQTL
rs9875617	RBM6	cis	cerebellum	SCAN
rs9875617	AMT	cis	parietal	SCAN
rs9875617	NICN1	cis	cerebellum	SCAN
rs9875617	RNF123	cis	parietal	SCAN
rs9875617	PARP3	cis	parietal	SCAN
rs9875617	IP6K2	cis	cerebellum	SCAN
rs9875617	RNF123	cis	cerebellum	SCAN
rs9875617	RBM6	Cis_1M	lymphoblastoid	RTeQTL
rs9875617	FAM212A	cis	Muscle Skeletal	GTEx
rs9875617	CISH	cis	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49630800-49636800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr3:49631000-49639600	Weak transcription	Muscle Satellite Cultured Cells	--

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