Variant report

Variant	rs9815103
Chromosome Location	chr3:48414215-48414216
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:48412970..48414853-chr3:48487087..48489637,2	K562	blood:

Variant related genes	Relation type
ENSG00000244380	Chromatin interaction
ENSG00000164053	Chromatin interaction

Extended variants
information (count: 94 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs1037773	1.00[CEU][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs10470686	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];0.91[MEX][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1109227	1.00[CEU][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs11130170	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11130171	1.00[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.91[TSI][hapmap];0.93[EUR][1000 genomes]
rs11712561	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11797	0.92[ASW][hapmap];0.82[CEU][hapmap];0.87[CHD][hapmap];0.97[GIH][hapmap];0.85[JPT][hapmap];0.97[LWK][hapmap];0.91[MKK][hapmap];0.82[TSI][hapmap];0.95[YRI][hapmap];0.82[EUR][1000 genomes]
rs12487542	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13069724	1.00[CEU][hapmap];0.97[GIH][hapmap];0.91[TSI][hapmap];0.89[YRI][hapmap];0.92[EUR][1000 genomes]
rs13071337	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13072012	0.86[EUR][1000 genomes]
rs13076076	1.00[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs13091785	0.85[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs13314659	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];0.91[MEX][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13324374	0.90[EUR][1000 genomes]
rs1459242	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1459249	0.92[EUR][1000 genomes]
rs1459250	0.86[EUR][1000 genomes]
rs1563736	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];0.91[MEX][hapmap];0.95[MKK][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1870444	0.88[EUR][1000 genomes]
rs1975844	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2045554	0.89[EUR][1000 genomes]
rs2242150	1.00[CEU][hapmap];0.87[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes]
rs2279077	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.97[LWK][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs2290822	1.00[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs2362450	1.00[CEU][hapmap];0.90[JPT][hapmap];0.93[EUR][1000 genomes]
rs2362452	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28824259	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2885509	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2885510	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3214041	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];0.86[MEX][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34761139	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35215722	0.87[EUR][1000 genomes]
rs3774808	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.97[LWK][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs4490383	0.88[EUR][1000 genomes]
rs4858793	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858795	0.82[CHD][hapmap];0.85[JPT][hapmap]
rs4858817	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858819	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs56298324	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60512868	0.92[EUR][1000 genomes]
rs6442116	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6442117	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.88[MKK][hapmap];0.83[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6442118	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6442119	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];0.91[MEX][hapmap];0.95[MKK][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6442120	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs6442123	0.89[EUR][1000 genomes]
rs6770470	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6776700	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.94[LWK][hapmap];0.93[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs6779262	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6784322	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6784541	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6794875	1.00[CEU][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.87[TSI][hapmap];0.93[EUR][1000 genomes]
rs6796491	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6800475	0.90[EUR][1000 genomes]
rs6804774	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6810060	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7126	0.87[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs725309	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs725310	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs730566	0.82[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap]
rs73074358	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs734071	0.87[CHD][hapmap];0.85[JPT][hapmap]
rs7618883	0.86[EUR][1000 genomes]
rs7630741	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7634377	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7635522	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7636044	0.96[CEU][hapmap];0.90[JPT][hapmap];0.90[EUR][1000 genomes]
rs7636782	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7639743	0.86[EUR][1000 genomes]
rs7651407	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.96[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap]
rs7653691	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs898225	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs922075	1.00[CEU][hapmap];0.87[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes]
rs9311423	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9311424	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9311428	0.87[CHD][hapmap];0.85[JPT][hapmap]
rs9809843	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9812647	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9826195	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9826247	0.85[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs9838618	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.97[LWK][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs9849509	1.00[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs9862575	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9864371	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9864815	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9875280	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9876781	1.00[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs9876891	0.87[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs9881491	0.85[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs9883759	1.00[CEU][hapmap];0.90[JPT][hapmap];0.91[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs9883927	1.00[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.91[TSI][hapmap];0.93[EUR][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	nsv834683	chr3:48301504-48493261	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	nsv834684	chr3:48385699-48589323	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs9815103	TREX1	Cis_1M	lymphoblastoid	RTeQTL
rs9815103	C3orf18	cis	cerebellum	SCAN
rs9815103	ALAS1	cis	parietal	SCAN
rs9815103	TMA7	cis	Muscle Skeletal	GTEx
rs9815103	ZNF589	cis	cerebellum	SCAN
rs9815103	SHISA5	cis	lymphoblastoid	seeQTL
rs9815103	CXCR6	cis	parietal	SCAN
rs9815103	AMT	cis	cerebellum	SCAN
rs9815103	NME6	cis	cerebellum	SCAN
rs9815103	ZNF589	cis	parietal	SCAN
rs9815103	AMT	cis	parietal	SCAN
rs9815103	RP11-24C3.2	cis	Muscle Skeletal	GTEx
rs9815103	SBK1	trans	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48409200-48414600	Weak transcription	K562	blood
2	chr3:48411800-48414400	Weak transcription	Fetal Intestine Small	intestine
3	chr3:48411800-48414800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr3:48412000-48414800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:48412200-48414400	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr3:48412200-48415000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr3:48413000-48415400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr3:48413800-48414600	Active TSS	Pancreas	Pancrea
9	chr3:48414000-48415200	Enhancers	Fetal Heart	heart
10	chr3:48414200-48415000	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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