Variant report

Variant	rs6916579
Chromosome Location	chr6:109851638-109851639
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 117 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:116)

rs_ID	r²[population]
rs10457192	0.86[CHB][hapmap];0.93[CHD][hapmap];0.90[MKK][hapmap];0.94[ASN][1000 genomes]
rs10457194	0.95[CHB][hapmap];0.87[JPT][hapmap];0.92[ASN][1000 genomes]
rs10457195	0.95[CHB][hapmap];0.87[JPT][hapmap];0.91[ASN][1000 genomes]
rs1048203	0.95[CEU][hapmap];0.81[CHB][hapmap];0.95[GIH][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap]
rs10499052	0.80[CEU][hapmap]
rs10499053	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10782162	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10782163	0.95[ASN][1000 genomes]
rs10872034	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11153171	0.82[CEU][hapmap]
rs11153174	0.95[CEU][hapmap];0.81[CHB][hapmap]
rs11153175	0.95[CEU][hapmap];0.80[CHB][hapmap]
rs11153183	0.95[CHB][hapmap];0.93[CHD][hapmap];0.87[JPT][hapmap];0.90[MKK][hapmap];0.94[ASN][1000 genomes]
rs11153188	0.90[ASN][1000 genomes]
rs11153213	0.94[CHB][hapmap]
rs11752791	0.88[ASN][1000 genomes]
rs11753645	0.89[CEU][hapmap]
rs11754340	0.86[ASN][1000 genomes]
rs11754455	0.95[CHB][hapmap];0.85[JPT][hapmap];0.94[ASN][1000 genomes]
rs11755641	0.95[CHB][hapmap];0.95[CHD][hapmap];0.87[JPT][hapmap];0.90[MKK][hapmap];0.87[ASN][1000 genomes]
rs11967108	0.95[CEU][hapmap];0.80[CHB][hapmap]
rs12190920	0.95[CEU][hapmap];0.84[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12190996	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12191353	0.82[ASN][1000 genomes]
rs12192268	0.90[CHB][hapmap];0.90[MKK][hapmap];0.86[YRI][hapmap]
rs12192776	0.83[ASN][1000 genomes]
rs12192847	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12193719	0.87[ASN][1000 genomes]
rs12194061	0.95[CHB][hapmap];0.87[JPT][hapmap];0.90[ASN][1000 genomes]
rs12194157	0.83[ASN][1000 genomes]
rs12197114	0.95[CEU][hapmap];0.81[CHB][hapmap]
rs12197180	0.95[CHB][hapmap];0.87[JPT][hapmap];0.93[ASN][1000 genomes]
rs12197950	0.83[ASN][1000 genomes]
rs12198938	0.95[CHB][hapmap];0.87[JPT][hapmap];0.94[ASN][1000 genomes]
rs12199154	0.95[CHB][hapmap];0.88[CHD][hapmap];0.87[JPT][hapmap];0.94[ASN][1000 genomes]
rs12204548	0.81[CHB][hapmap];0.90[MKK][hapmap];0.86[YRI][hapmap]
rs12205485	0.86[ASN][1000 genomes]
rs12208018	0.86[ASN][1000 genomes]
rs12208933	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12209691	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12212476	0.95[CHB][hapmap];0.86[JPT][hapmap];0.94[ASN][1000 genomes]
rs12214639	0.87[ASN][1000 genomes]
rs12524502	0.85[CEU][hapmap]
rs12524639	0.95[CEU][hapmap];0.81[CHB][hapmap]
rs12528712	0.90[CEU][hapmap];0.93[MKK][hapmap]
rs12528781	0.86[ASN][1000 genomes]
rs12528822	0.95[CEU][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap]
rs12529505	0.80[CEU][hapmap]
rs13191066	0.86[ASN][1000 genomes]
rs13195517	0.90[CEU][hapmap]
rs13199135	0.87[ASN][1000 genomes]
rs13199519	0.90[CEU][hapmap]
rs13201947	0.88[ASN][1000 genomes]
rs13201951	0.92[ASN][1000 genomes]
rs13203252	0.89[CEU][hapmap]
rs13203587	0.94[ASN][1000 genomes]
rs13204102	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13204500	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13204787	0.80[CEU][hapmap]
rs13211604	0.84[CEU][hapmap]
rs1321328	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13220304	0.80[CEU][hapmap];0.81[MKK][hapmap]
rs13220915	0.95[CHB][hapmap];0.86[JPT][hapmap];0.94[ASN][1000 genomes]
rs1358998	0.95[CEU][hapmap];0.81[CHB][hapmap];0.95[GIH][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap]
rs1406899	0.95[CHB][hapmap];0.87[JPT][hapmap];0.94[ASN][1000 genomes]
rs1476388	0.95[ASN][1000 genomes]
rs1546980	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17070580	0.90[CEU][hapmap];0.88[GIH][hapmap]
rs1923725	0.95[CEU][hapmap];0.81[CHB][hapmap]
rs1960325	0.87[ASN][1000 genomes]
rs1980591	0.95[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs1998811	0.94[ASN][1000 genomes]
rs2024849	0.94[ASN][1000 genomes]
rs2024850	0.95[CHB][hapmap];0.93[CHD][hapmap];0.87[JPT][hapmap];0.94[ASN][1000 genomes]
rs2024852	0.94[ASN][1000 genomes]
rs2024853	0.86[CHB][hapmap];0.82[JPT][hapmap];0.94[ASN][1000 genomes]
rs2025148	0.90[CHB][hapmap];0.90[MKK][hapmap];0.86[YRI][hapmap]
rs2148089	0.90[AFR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2208209	0.93[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2236582	0.90[CEU][hapmap];0.81[CHB][hapmap];0.95[GIH][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap]
rs2275650	0.95[CEU][hapmap];0.95[GIH][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap]
rs2277114	0.95[CHB][hapmap];0.95[CHD][hapmap];0.87[JPT][hapmap];0.94[ASN][1000 genomes]
rs2357124	0.88[ASN][1000 genomes]
rs3757234	0.95[CEU][hapmap];0.81[CHB][hapmap]
rs3778477	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3799835	0.90[CEU][hapmap]
rs3799845	0.90[CHB][hapmap];0.86[YRI][hapmap]
rs3799849	0.85[CHB][hapmap];0.90[MKK][hapmap]
rs3807005	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3899233	0.95[CHB][hapmap];0.95[CHD][hapmap];0.87[JPT][hapmap];0.90[MKK][hapmap]
rs4490694	0.87[ASN][1000 genomes]
rs4945833	0.87[ASN][1000 genomes]
rs59056467	0.80[AMR][1000 genomes]
rs68042406	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6906216	0.92[ASN][1000 genomes]
rs6911700	0.95[CHB][hapmap];0.95[CHD][hapmap];0.87[JPT][hapmap];0.91[MKK][hapmap]
rs6911838	0.90[CEU][hapmap]
rs6914498	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6920292	0.85[ASN][1000 genomes]
rs6920962	0.82[CEU][hapmap]
rs6926096	0.92[ASN][1000 genomes]
rs729888	0.95[CHB][hapmap];0.87[JPT][hapmap];0.90[MKK][hapmap];0.83[ASN][1000 genomes]
rs749517	0.95[ASN][1000 genomes]
rs752262	0.80[CHB][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7755941	0.90[CHB][hapmap];0.93[CHD][hapmap];0.81[JPT][hapmap];0.94[ASN][1000 genomes]
rs7767525	0.81[ASN][1000 genomes]
rs7773095	0.95[CEU][hapmap];0.81[CHB][hapmap];0.95[GIH][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap]
rs7773950	0.95[CHB][hapmap];0.87[JPT][hapmap];0.94[ASN][1000 genomes]
rs9320287	0.90[CEU][hapmap];0.88[GIH][hapmap]
rs9480948	0.95[CEU][hapmap];0.81[CHB][hapmap];0.95[GIH][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap]
rs9480953	0.90[CEU][hapmap]
rs9480957	0.95[CEU][hapmap];0.81[CHB][hapmap];0.95[GIH][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap]
rs9487094	0.90[CEU][hapmap];0.88[GIH][hapmap]
rs9487100	0.95[CEU][hapmap];0.80[CHB][hapmap]
rs971434	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9885646	0.90[CEU][hapmap];0.88[GIH][hapmap]

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	nsv1026012	chr6:109851638-109999379	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs6916579	SMPD2	cis	multi-tissue	Pritchard
rs6916579	SMPD2	cis	parietal	SCAN
rs6916579	RP11-425D10.10	cis	Esophagus Mucosa	GTEx
rs6916579	PPIL6	cis	cerebellum	SCAN
rs6916579	AKD1	cis	cerebellum	SCAN
rs6916579	RP11-425D10.10	cis	Skin Sun Exposed Lower leg	GTEx
rs6916579	FIG4	cis	parietal	SCAN
rs6916579	SMPD2	cis	Whole Blood	GTEx
rs6916579	CD164	cis	parietal	SCAN
rs6916579	MICAL1	cis	parietal	SCAN
rs6916579	SMPD2	cis	cerebellum	SCAN
rs6916579	PDSS2	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:109838600-109861400	Weak transcription	Thymus	Thymus
2	chr6:109848400-109865600	Weak transcription	Aorta	Aorta
3	chr6:109848400-109870400	Weak transcription	Primary B cells from peripheral blood	blood
4	chr6:109850800-109870000	Weak transcription	Left Ventricle	heart
5	chr6:109851000-109853000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr6:109851400-109854400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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