Variant report

Variant	rs1323626
Chromosome Location	chr1:93863897-93863898
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 138 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:137)

rs_ID	r²[population]
rs1000606	0.88[EUR][1000 genomes]
rs10430073	0.88[EUR][1000 genomes]
rs10782958	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1081523	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1081524	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1081525	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1081526	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10874765	1.00[CEU][hapmap];0.89[YRI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10874767	1.00[CEU][hapmap];0.96[TSI][hapmap];0.89[EUR][1000 genomes]
rs10874771	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10874774	0.83[EUR][1000 genomes]
rs10874775	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11164878	0.87[AMR][1000 genomes]
rs11164882	0.87[AMR][1000 genomes]
rs11164888	0.89[EUR][1000 genomes]
rs11164889	0.89[EUR][1000 genomes]
rs11164890	0.89[EUR][1000 genomes]
rs11164891	0.85[EUR][1000 genomes]
rs11164906	0.88[EUR][1000 genomes]
rs11164911	1.00[CEU][hapmap];0.96[TSI][hapmap];0.93[EUR][1000 genomes]
rs11582703	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11584466	0.88[EUR][1000 genomes]
rs12070900	0.84[CEU][hapmap];0.83[YRI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12071627	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12080715	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12085959	1.00[CEU][hapmap];0.87[YRI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12088338	0.84[AMR][1000 genomes]
rs12090723	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12731675	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12731809	0.90[EUR][1000 genomes]
rs1323627	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1323628	0.91[ASW][hapmap];1.00[CEU][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1414367	0.87[AMR][1000 genomes]
rs1535698	1.00[CEU][hapmap];0.89[YRI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1535700	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs1570528	1.00[CEU][hapmap];0.96[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2031223	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2031224	0.88[EUR][1000 genomes]
rs2104280	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2484485	0.87[AMR][1000 genomes]
rs2783492	0.87[AMR][1000 genomes]
rs2783498	0.92[CEU][hapmap];0.93[YRI][hapmap];0.87[AMR][1000 genomes]
rs2783506	0.87[AMR][1000 genomes]
rs2815408	0.87[AMR][1000 genomes]
rs2815409	0.87[AMR][1000 genomes]
rs2815410	0.87[AMR][1000 genomes]
rs2815411	0.87[AMR][1000 genomes]
rs2815412	0.84[AMR][1000 genomes]
rs2815413	1.00[CEU][hapmap]
rs4573531	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4847239	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4847407	0.88[EUR][1000 genomes]
rs4847409	1.00[CEU][hapmap];0.96[TSI][hapmap];0.88[EUR][1000 genomes]
rs4847411	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs485622	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs488646	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs504810	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs505531	0.87[AMR][1000 genomes]
rs506556	1.00[CEU][hapmap];0.96[TSI][hapmap]
rs508942	0.86[EUR][1000 genomes]
rs512361	0.88[EUR][1000 genomes]
rs519723	1.00[CEU][hapmap];0.96[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs522999	1.00[CEU][hapmap]
rs523262	0.86[EUR][1000 genomes]
rs546	0.87[AMR][1000 genomes]
rs556888	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs558667	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs559397	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56303209	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs566743	0.83[EUR][1000 genomes]
rs571212	1.00[CEU][hapmap];0.92[TSI][hapmap];0.80[EUR][1000 genomes]
rs573056	1.00[CEU][hapmap];0.96[TSI][hapmap]
rs581825	1.00[CEU][hapmap]
rs587754	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs605759	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs626714	1.00[CEU][hapmap];0.96[TSI][hapmap];0.89[EUR][1000 genomes]
rs628714	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs629153	1.00[CEU][hapmap];0.89[YRI][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs631966	0.88[EUR][1000 genomes]
rs633789	0.93[CEU][hapmap];0.92[TSI][hapmap];0.88[EUR][1000 genomes]
rs637198	0.86[EUR][1000 genomes]
rs641390	0.86[EUR][1000 genomes]
rs6541351	0.90[ASW][hapmap];1.00[CEU][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6541400	0.88[EUR][1000 genomes]
rs658178	1.00[CEU][hapmap];0.89[YRI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs658877	1.00[CEU][hapmap]
rs661566	0.82[EUR][1000 genomes]
rs662546	0.82[EUR][1000 genomes]
rs6657587	0.89[EUR][1000 genomes]
rs6664886	1.00[CEU][hapmap];0.85[YRI][hapmap];0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6667701	1.00[CEU][hapmap];0.96[TSI][hapmap];0.89[EUR][1000 genomes]
rs667680	0.92[AMR][1000 genomes]
rs6687359	0.88[EUR][1000 genomes]
rs668944	1.00[CEU][hapmap];0.96[TSI][hapmap];0.85[EUR][1000 genomes]
rs6701250	1.00[CEU][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs670650	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs671559	0.87[AMR][1000 genomes]
rs693872	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs698926	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7413775	0.88[EUR][1000 genomes]
rs7519163	1.00[CEU][hapmap];0.96[TSI][hapmap];0.88[EUR][1000 genomes]
rs7525189	0.88[EUR][1000 genomes]
rs7529639	0.96[EUR][1000 genomes]
rs7546661	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7551635	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7555292	0.91[ASW][hapmap];1.00[CEU][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs771448	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs771449	0.96[EUR][1000 genomes]
rs771450	0.96[EUR][1000 genomes]
rs771451	0.96[EUR][1000 genomes]
rs771452	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs771453	0.96[EUR][1000 genomes]
rs771455	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs771456	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs771457	1.00[CEU][hapmap];0.94[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs771459	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs771460	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs771463	1.00[CEU][hapmap];0.96[TSI][hapmap];0.93[EUR][1000 genomes]
rs771464	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs771466	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs771467	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs771468	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs771469	1.00[CEU][hapmap];0.92[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs771471	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs771472	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs771474	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs771475	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs771477	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs771480	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs797660	0.87[AMR][1000 genomes]
rs797669	0.81[EUR][1000 genomes]
rs809515	0.80[EUR][1000 genomes]
rs810028	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs812789	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9432680	0.87[EUR][1000 genomes]
rs9432700	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9432701	0.87[EUR][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	nsv871640	chr1:93807122-93953469	Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs1323626	RP4-717I23.3	cis	Heart Left Ventricle	GTEx
rs1323626	TMED5	cis	parietal	SCAN
rs1323626	TMED5	cis	cerebellum	SCAN
rs1323626	RP4-717I23.3	cis	Esophagus Muscularis	GTEx
rs1323626	TMED5	Cis_1M	lymphoblastoid	RTeQTL
rs1323626	RP4-717I23.3	cis	Stomach	GTEx
rs1323626	RP4-717I23.3	cis	Artery Aorta	GTEx
rs1323626	RP4-717I23.3	cis	Thyroid	GTEx
rs1323626	RP4-717I23.3	cis	Esophagus Mucosa	GTEx
rs1323626	RP4-717I23.3	cis	Nerve Tibial	GTEx
rs1323626	RP4-717I23.3	cis	lung	GTEx
rs1323626	RP4-717I23.3	cis	Skin Sun Exposed Lower leg	GTEx
rs1323626	RP4-717I23.3	cis	Muscle Skeletal	GTEx
rs1323626	RP4-717I23.3	cis	Adipose Subcutaneous	GTEx
rs1323626	RP4-717I23.3	cis	Whole Blood	GTEx
rs1323626	RP4-717I23.3	cis	Artery Tibial	GTEx
rs1323626	LOC646848	cis	normal skin	skin_eQTL

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93853200-93866000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:93861000-93865400	Weak transcription	HMEC	breast
3	chr1:93861200-93865200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:93861800-93865200	Weak transcription	NHEK	skin
5	chr1:93862000-93865400	Weak transcription	HepG2	liver

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