Variant report

Variant	rs1459242
Chromosome Location	chr3:48413537-48413538
allele	C/T
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: 12 )

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

rs_ID	r²[population]
rs1037773	1.00[CEU][hapmap];0.95[JPT][hapmap];0.91[EUR][1000 genomes]
rs10470686	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];0.89[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1109227	1.00[CEU][hapmap];0.95[JPT][hapmap];0.91[EUR][1000 genomes]
rs11130170	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11130171	1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap];0.92[EUR][1000 genomes]
rs11712561	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11797	0.82[CEU][hapmap];0.84[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.80[MKK][hapmap];0.81[EUR][1000 genomes]
rs12487542	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13069724	1.00[CEU][hapmap];0.97[GIH][hapmap];0.87[TSI][hapmap];0.91[EUR][1000 genomes]
rs13071337	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13072012	0.85[EUR][1000 genomes]
rs13076076	1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes]
rs13091785	0.88[EUR][1000 genomes]
rs13314659	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];0.89[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13324374	0.89[EUR][1000 genomes]
rs1459249	0.91[EUR][1000 genomes]
rs1459250	0.85[EUR][1000 genomes]
rs1563736	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];0.89[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1870444	0.87[EUR][1000 genomes]
rs1975844	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2045554	0.88[EUR][1000 genomes]
rs2242150	1.00[CEU][hapmap];0.84[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes]
rs2279077	1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.82[MKK][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes]
rs2290822	1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes]
rs2362450	1.00[CEU][hapmap];0.95[JPT][hapmap];0.92[EUR][1000 genomes]
rs2362452	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28824259	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2885509	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2885510	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3214041	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[MKK][hapmap];0.89[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34761139	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35215722	0.85[EUR][1000 genomes]
rs3774808	1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.82[MKK][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes]
rs4490383	0.88[EUR][1000 genomes]
rs4858793	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858795	0.80[CHD][hapmap];0.90[JPT][hapmap]
rs4858817	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858819	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs56298324	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60512868	0.91[EUR][1000 genomes]
rs6442116	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6442117	0.86[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6442118	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6442119	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6442120	1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.85[MKK][hapmap];0.84[TSI][hapmap];0.92[EUR][1000 genomes]
rs6442123	0.88[EUR][1000 genomes]
rs6770470	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6776700	1.00[CEU][hapmap];0.84[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.82[MKK][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes]
rs6779262	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6784322	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6784541	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6794875	1.00[CEU][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.86[TSI][hapmap];0.92[EUR][1000 genomes]
rs6796491	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6800475	0.88[EUR][1000 genomes]
rs6804774	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6810060	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7126	0.89[EUR][1000 genomes]
rs725309	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs725310	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];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs730566	0.82[CHB][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap]
rs73074358	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs734071	0.85[CHD][hapmap];0.90[JPT][hapmap]
rs7618883	0.84[EUR][1000 genomes]
rs7630741	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7634377	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7635522	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7636044	0.96[CEU][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes]
rs7636782	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7639743	0.84[EUR][1000 genomes]
rs7651407	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];0.87[TSI][hapmap]
rs7653691	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs898225	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs922075	1.00[CEU][hapmap];0.84[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes]
rs9311423	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9311424	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9311428	0.85[CHD][hapmap];0.90[JPT][hapmap]
rs9809843	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9812647	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9815103	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]
rs9826195	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9826247	0.87[EUR][1000 genomes]
rs9838618	1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.82[MKK][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes]
rs9849509	1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes]
rs9862575	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9864371	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9864815	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9875280	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9876781	1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes]
rs9876891	0.91[EUR][1000 genomes]
rs9881491	0.88[EUR][1000 genomes]
rs9883759	1.00[CEU][hapmap];0.95[JPT][hapmap];0.92[EUR][1000 genomes]
rs9883927	1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap];0.92[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:12)

SNP	Gene	Cis/trans	Tissue	Source
rs1459242	SBK1	trans	cerebellum	SCAN
rs1459242	CXCR6	cis	parietal	SCAN
rs1459242	TMA7	cis	Muscle Skeletal	GTEx
rs1459242	TREX1	Cis_1M	lymphoblastoid	RTeQTL
rs1459242	C3orf18	cis	cerebellum	SCAN
rs1459242	NME6	cis	cerebellum	SCAN
rs1459242	ALAS1	cis	parietal	SCAN
rs1459242	AMT	cis	cerebellum	SCAN
rs1459242	AMT	cis	parietal	SCAN
rs1459242	RP11-24C3.2	cis	Muscle Skeletal	GTEx
rs1459242	ZNF589	cis	parietal	SCAN
rs1459242	ZNF589	cis	cerebellum	SCAN

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

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

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