Variant report

Variant	rs1316657
Chromosome Location	chr17:46251391-46251392
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	chr17:46228679..46233044-chr17:46249536..46252436,3	K562	blood:

Extended variants
information (count: 136 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:135)

rs_ID	r²[population]
rs1002330	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1010228	0.85[CHB][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs1010230	0.80[ASN][1000 genomes]
rs10445339	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10445377	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10853098	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11079806	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs11079808	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs11079809	0.80[ASN][1000 genomes]
rs11079814	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11651097	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs11870056	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11872095	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12150533	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12452956	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12603115	0.92[CEU][hapmap];0.81[CHB][hapmap];0.86[CHD][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12603380	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12936369	0.82[ASN][1000 genomes]
rs12936731	0.92[CHB][hapmap];0.81[JPT][hapmap]
rs12941830	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12947089	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12948810	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12952670	0.82[EUR][1000 genomes]
rs1377201	0.88[ASW][hapmap];0.90[MKK][hapmap];0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1452662	0.80[ASN][1000 genomes]
rs1452663	0.84[CHB][hapmap];0.87[JPT][hapmap];0.80[ASN][1000 genomes]
rs1452665	0.85[CHB][hapmap];0.87[JPT][hapmap];0.80[ASN][1000 genomes]
rs1452666	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1452667	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1468270	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs16951519	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs16953927	0.80[ASN][1000 genomes]
rs16953941	0.85[CHB][hapmap];0.87[JPT][hapmap];0.80[ASN][1000 genomes]
rs16954268	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs16954324	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs17620033	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17681336	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1860862	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1860863	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1860866	0.80[ASN][1000 genomes]
rs1979897	0.85[CHB][hapmap]
rs2021752	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2021811	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2041572	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2051821	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs2060876	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2072441	0.87[CEU][hapmap];0.81[CHB][hapmap]
rs208005	0.85[CHB][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs208008	0.85[CHB][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs208009	0.85[CHB][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs208011	0.82[ASN][1000 genomes]
rs208012	0.82[ASN][1000 genomes]
rs208015	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs208019	0.84[ASN][1000 genomes]
rs2109982	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2109983	0.80[JPT][hapmap];0.80[ASN][1000 genomes]
rs2109984	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs2123341	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2229369	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs2240120	0.85[CHB][hapmap]
rs2240121	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs2240122	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs2278868	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2305433	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2325784	0.83[ASN][1000 genomes]
rs2325804	0.85[CHB][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs2325885	0.80[ASN][1000 genomes]
rs2924257	0.90[CEU][hapmap];0.86[CHB][hapmap]
rs2938483	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34949267	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34980108	0.80[ASN][1000 genomes]
rs36071506	0.80[ASN][1000 genomes]
rs3744346	0.85[CHB][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs3792692	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3792694	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3805363	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3805370	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3805371	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3815472	0.84[ASN][1000 genomes]
rs3897986	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3944039	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4793779	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4794447	1.00[CHB][hapmap];0.87[JPT][hapmap];0.89[ASN][1000 genomes]
rs4794451	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs4794505	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4794517	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4794525	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55696440	0.82[ASN][1000 genomes]
rs55982346	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62066407	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62066447	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6504025	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs6504108	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs66683298	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs67446770	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6847	0.81[JPT][hapmap]
rs71356521	0.82[ASN][1000 genomes]
rs7209730	0.80[ASN][1000 genomes]
rs7210149	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7212202	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs7213876	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7217496	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs7219967	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7220619	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7220768	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7220922	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7222136	0.85[CHB][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs7223867	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7224014	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs7224461	0.80[ASN][1000 genomes]
rs7225435	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7225550	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7225865	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs741058	0.80[ASN][1000 genomes]
rs7501770	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs758999	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8065670	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs8066391	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs8069064	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8069263	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8071199	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs8071879	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs8072282	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8075270	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8077860	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs8079616	0.84[ASN][1000 genomes]
rs875065	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs882380	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs954226	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs978263	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs9807087	0.80[ASN][1000 genomes]
rs9899275	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs9899461	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs9903692	0.82[ASN][1000 genomes]
rs9909933	0.80[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	nsv908576	chr17:46147807-46260366	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs1316657	PRAC	cis	parietal	SCAN
rs1316657	CBX1	cis	cerebellum	SCAN
rs1316657	SNX11	cis	Lymphoblastoid	GTEx
rs1316657	AARSD1	cis	parietal	SCAN
rs1316657	CDK5RAP3	cis	parietal	SCAN
rs1316657	CDK5RAP3	cis	cerebellum	SCAN
rs1316657	EIF1	cis	cerebellum	SCAN
rs1316657	SNX11	cis	parietal	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46216400-46251400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr17:46239200-46253800	Weak transcription	Primary B cells from peripheral blood	blood
3	chr17:46241000-46253200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr17:46245000-46252200	Weak transcription	GM12878-XiMat	blood
5	chr17:46247000-46258600	Weak transcription	Primary B cells from cord blood	blood
6	chr17:46247400-46253000	Weak transcription	Thymus	Thymus
7	chr17:46247800-46254400	Weak transcription	Fetal Thymus	thymus
8	chr17:46248000-46253000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr17:46248200-46253000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr17:46250000-46253000	Enhancers	HSMM	muscle
11	chr17:46250200-46251800	Genic enhancers	Primary T cells fromperipheralblood	blood
12	chr17:46250200-46252600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
13	chr17:46250200-46253000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr17:46250200-46255200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr17:46250400-46251800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr17:46250400-46251800	Enhancers	Primary T helper cells PMA-I stimulated	--
17	chr17:46250400-46251800	Enhancers	Primary T killer memory cells from peripheral blood	blood
18	chr17:46250400-46252800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr17:46250600-46252400	Weak transcription	Primary hematopoietic stem cells	blood
20	chr17:46250800-46251800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr17:46250800-46251800	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
22	chr17:46250800-46252000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr17:46251000-46257400	Enhancers	HSMMtube	muscle
24	chr17:46251200-46253600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr17:46251200-46254400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr17:46251200-46267200	Strong transcription	Primary T cells from cord blood	blood
27	chr17:46251200-46277400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

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