Variant report

Variant	rs4685409
Chromosome Location	chr3:17000910-17000911
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:16999677..17001737-chr3:17018977..17021137,2	K562	blood:

Extended variants
information (count: 91 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10865746	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11128813	0.81[CHD][hapmap]
rs11128815	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11717329	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11926952	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12108065	0.82[CHD][hapmap]
rs12233492	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12487288	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12497667	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12497953	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13058764	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13059347	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13071645	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13080108	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13080782	0.94[EUR][1000 genomes]
rs13317381	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1348109	0.82[ASN][1000 genomes]
rs1441035	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1441039	0.83[ASN][1000 genomes]
rs17272796	0.85[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1806555	1.00[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1806556	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1837697	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1837698	0.83[ASN][1000 genomes]
rs2014490	0.86[JPT][hapmap]
rs34149515	0.82[ASN][1000 genomes]
rs35319117	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3796299	0.81[CHD][hapmap]
rs3906814	0.95[CEU][hapmap];0.84[JPT][hapmap];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3924971	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4131153	0.81[CHD][hapmap]
rs4234539	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4289331	0.80[CHD][hapmap]
rs4295151	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4334629	0.85[CEU][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap];0.91[TSI][hapmap]
rs4353792	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4383507	0.81[CHD][hapmap]
rs4402923	0.81[CHD][hapmap]
rs4423750	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4461404	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4472039	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4535211	0.81[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.96[MEX][hapmap];0.95[MKK][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4561816	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4563393	0.89[YRI][hapmap]
rs4596131	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4602367	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4618210	0.81[CHD][hapmap];0.85[JPT][hapmap];0.86[YRI][hapmap]
rs4684307	0.80[CHD][hapmap]
rs4684308	0.81[JPT][hapmap]
rs4685404	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4685405	0.86[JPT][hapmap]
rs4685408	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4685415	0.81[AMR][1000 genomes]
rs4685418	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4685420	0.88[CEU][hapmap];0.80[YRI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4685421	0.89[CEU][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4685422	0.86[YRI][hapmap]
rs4685426	0.90[JPT][hapmap]
rs4685427	0.85[JPT][hapmap]
rs55748719	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6442660	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs6762816	0.89[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6776032	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6780191	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6781611	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6797029	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6805534	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6807144	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6809087	0.81[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.96[MEX][hapmap];0.95[MKK][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7610811	0.89[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.86[YRI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7611127	0.81[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.96[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7612044	0.89[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7617672	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7629171	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7645335	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7648912	0.82[CHD][hapmap]
rs7653027	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7653834	0.82[CHD][hapmap]
rs9810017	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9824172	0.86[JPT][hapmap]
rs9830460	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9841259	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9844888	0.87[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs9854760	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9862613	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9879150	0.95[JPT][hapmap]
rs9880307	0.81[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs9881521	0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9883633	0.89[JPT][hapmap]
rs9985404	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][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	nsv980048	chr3:16995372-17016178	Weak transcription Enhancers ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4685409	PLCL2	cis	Whole Blood	GTEx
rs4685409	CHCHD4	cis	parietal	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:16984200-17003400	Weak transcription	Spleen	Spleen
2	chr3:16985000-17003400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr3:16986800-17003000	Weak transcription	Ovary	ovary
4	chr3:16987400-17005000	Weak transcription	Primary B cells from cord blood	blood
5	chr3:16987400-17015600	Weak transcription	Aorta	Aorta
6	chr3:16993400-17003400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr3:16993400-17005200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr3:16993800-17002200	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr3:16999400-17003000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr3:16999600-17001200	Enhancers	Primary T helper naive cells from peripheral blood	blood
11	chr3:17000000-17002800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr3:17000400-17001200	Enhancers	Fetal Heart	heart
13	chr3:17000400-17001400	Strong transcription	Primary T cells from cord blood	blood
14	chr3:17000400-17002000	Enhancers	Left Ventricle	heart
15	chr3:17000600-17002200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr3:17000600-17003000	Weak transcription	Pancreas	Pancrea
17	chr3:17000600-17003000	Weak transcription	Psoas Muscle	Psoas
18	chr3:17000600-17003000	Weak transcription	Right Atrium	heart
19	chr3:17000600-17008400	Weak transcription	Primary hematopoietic stem cells	blood
20	chr3:17000800-17002800	Weak transcription	Right Ventricle	heart
21	chr3:17000800-17003000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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