Variant report

Variant	rs10004745
Chromosome Location	chr4:173394997-173394998
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 127 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:121)

rs_ID	r²[population]
rs10008531	0.83[CEU][hapmap]
rs10019934	0.90[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs10024431	0.81[JPT][hapmap]
rs10029297	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10434403	0.90[CHB][hapmap];0.85[CHD][hapmap];0.94[JPT][hapmap]
rs11132944	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11132945	0.92[ASN][1000 genomes]
rs11132946	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12498714	0.91[CEU][hapmap]
rs12506997	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.81[JPT][hapmap];0.83[LWK][hapmap];0.80[MEX][hapmap];0.91[TSI][hapmap]
rs12510279	0.91[CEU][hapmap]
rs13144858	0.83[CEU][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs13435174	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs1355009	0.82[CEU][hapmap]
rs1396222	0.86[TSI][hapmap]
rs1455126	1.00[ASW][hapmap];0.92[CEU][hapmap];0.81[CHB][hapmap];0.80[MEX][hapmap]
rs1496710	0.84[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap]
rs1508257	0.86[TSI][hapmap]
rs163185	0.83[CEU][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap]
rs17058323	0.83[CEU][hapmap]
rs170776	0.83[CEU][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap]
rs1869684	0.85[CEU][hapmap];0.80[MEX][hapmap]
rs1874504	0.84[CEU][hapmap]
rs1874505	0.84[CHB][hapmap]
rs1995068	0.90[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs2047342	0.90[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap]
rs2332482	0.83[CEU][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap]
rs2332519	0.85[CEU][hapmap]
rs2332535	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs2654786	1.00[YRI][hapmap]
rs2877713	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs3104246	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs333377	0.82[CEU][hapmap]
rs333378	0.83[CEU][hapmap]
rs333379	0.82[CEU][hapmap]
rs333400	0.83[CEU][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap]
rs335966	0.91[CEU][hapmap]
rs335969	0.83[CEU][hapmap];0.85[JPT][hapmap]
rs335970	0.82[CEU][hapmap];0.86[JPT][hapmap]
rs335972	0.81[CHD][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes]
rs335973	0.83[CEU][hapmap];0.81[JPT][hapmap]
rs335975	0.83[CEU][hapmap];0.86[JPT][hapmap]
rs335977	0.91[CEU][hapmap]
rs335979	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs335980	0.91[CEU][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap]
rs335981	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs335982	0.91[CEU][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs335983	0.91[CEU][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs335984	0.81[EUR][1000 genomes]
rs335985	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs335986	1.00[CEU][hapmap]
rs335987	0.91[CEU][hapmap]
rs335989	0.91[CEU][hapmap];1.00[YRI][hapmap]
rs335991	0.83[CEU][hapmap];0.84[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap]
rs335993	0.83[CEU][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap]
rs335995	0.83[CEU][hapmap]
rs335997	0.81[EUR][1000 genomes]
rs335998	0.91[CEU][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap]
rs336000	0.91[CEU][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs336001	0.86[CEU][hapmap]
rs336002	0.92[CEU][hapmap];0.87[JPT][hapmap]
rs336003	0.81[JPT][hapmap]
rs336005	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs336006	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs336014	0.92[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]
rs336016	0.92[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]
rs336017	0.92[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]
rs336018	0.92[CEU][hapmap]
rs336019	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs336021	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs336022	0.92[CEU][hapmap]
rs337017	0.91[CEU][hapmap]
rs337018	0.91[CEU][hapmap]
rs337045	0.91[CEU][hapmap];0.86[GIH][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap]
rs337050	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs337051	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs337053	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs337984	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs337985	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs337986	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs337988	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs337989	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs337990	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs337991	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs337992	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs337993	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs337995	1.00[CEU][hapmap];0.84[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.80[EUR][1000 genomes]
rs337997	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap]
rs337999	0.92[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.81[JPT][hapmap];0.80[MEX][hapmap];0.91[TSI][hapmap]
rs338004	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs338007	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs338017	1.00[YRI][hapmap]
rs338021	0.81[CHB][hapmap]
rs338027	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs338028	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs338029	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs338030	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs338033	1.00[CEU][hapmap]
rs4247207	0.83[CHB][hapmap]
rs455869	0.91[CEU][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap]
rs462761	0.91[CEU][hapmap]
rs466124	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs4692651	0.89[MEX][hapmap];0.81[TSI][hapmap]
rs488103	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6553632	0.81[MEX][hapmap];0.86[TSI][hapmap]
rs663643	0.91[CEU][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap]
rs6815640	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6816068	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs6819214	1.00[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap]
rs6821570	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6838976	0.91[MEX][hapmap];0.86[TSI][hapmap]
rs6844055	0.81[CEU][hapmap]
rs6844483	0.85[CEU][hapmap]
rs720635	0.92[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.81[JPT][hapmap];0.80[MEX][hapmap];0.91[TSI][hapmap]
rs744774	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap]
rs744775	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7670427	0.92[CEU][hapmap]
rs7677902	0.83[CEU][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap]
rs7691982	0.91[CEU][hapmap]
rs7699264	1.00[CEU][hapmap];0.95[CHB][hapmap]
rs961306	0.85[CEU][hapmap];0.80[MEX][hapmap]

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	nsv1031592	chr4:173112542-173662991	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv537359	chr4:173112542-173662991	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv534293	chr4:173121379-173606082	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1031327	chr4:173306405-173465248	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv508333	chr4:173369686-173447675	ZNF genes & repeats Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv948856	chr4:173388217-173967546	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10004745	MPP3	trans	brain	seeQTL
rs10004745	KCTD14	trans	brain	seeQTL
rs10004745	ESPNL	trans	brain	seeQTL
rs10004745	EOMES	trans	brain	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:173394000-173395000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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