Variant report

Variant	rs16954268
Chromosome Location	chr17:46319546-46319547
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:46297106..46299092-chr17:46317071..46320031,2	K562	blood:
2	chr17:46304702..46306804-chr17:46316986..46319945,3	K562	blood:
3	chr17:46317007..46319839-chr17:46328201..46331501,3	K562	blood:
4	chr17:46312738..46316050-chr17:46317088..46320426,4	K562	blood:
5	chr17:46316932..46321831-chr17:46322420..46326261,9	K562	blood:
6	chr17:46297106..46299092-chr17:46317071..46320404,3	K562	blood:
7	chr17:46305304..46308204-chr17:46318445..46319954,2	K562	blood:

Extended variants
information (count: 119 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:119)

rs_ID	r²[population]
rs1010228	1.00[CHB][hapmap];0.91[CHD][hapmap];0.93[JPT][hapmap]
rs1010230	0.81[EUR][1000 genomes]
rs10514944	0.89[TSI][hapmap]
rs11079806	1.00[CHB][hapmap];0.86[CHD][hapmap];0.93[JPT][hapmap]
rs11079808	1.00[CHB][hapmap];0.91[CHD][hapmap];0.93[JPT][hapmap]
rs11651097	1.00[CHB][hapmap];0.91[CHD][hapmap];0.93[JPT][hapmap]
rs12936369	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12936731	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs12939334	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12941352	0.82[YRI][hapmap]
rs12946208	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12946679	0.82[YRI][hapmap]
rs12947089	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs12948214	1.00[YRI][hapmap]
rs12950437	0.82[YRI][hapmap]
rs1316657	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs1377201	0.83[ASN][1000 genomes]
rs1452662	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1452663	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1452665	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1452666	0.85[CHB][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs1452667	0.85[CHB][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs1468270	1.00[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap]
rs16951519	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs16952687	1.00[YRI][hapmap]
rs16953927	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16953941	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16954324	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16955960	0.89[TSI][hapmap]
rs17620033	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs17620866	0.85[EUR][1000 genomes]
rs17621689	0.85[EUR][1000 genomes]
rs17623518	0.84[TSI][hapmap]
rs17693878	0.84[EUR][1000 genomes]
rs17694092	0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs17694168	0.85[EUR][1000 genomes]
rs17694404	0.95[TSI][hapmap];0.85[EUR][1000 genomes]
rs17694670	0.85[EUR][1000 genomes]
rs17695179	0.80[EUR][1000 genomes]
rs1860862	0.85[CHB][hapmap];0.80[JPT][hapmap]
rs1979897	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2021752	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs2023885	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs2036520	0.85[EUR][1000 genomes]
rs2036521	0.85[EUR][1000 genomes]
rs2041572	0.85[CHB][hapmap];0.80[JPT][hapmap]
rs2051821	1.00[CHB][hapmap];0.91[CHD][hapmap];0.93[JPT][hapmap]
rs2060876	0.85[CHB][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs208005	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs208008	1.00[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs208009	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs208011	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs208012	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs208015	1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.80[ASN][1000 genomes]
rs208019	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2109982	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs2109983	0.89[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs2109984	1.00[CHB][hapmap];0.91[CHD][hapmap];0.93[JPT][hapmap]
rs2123341	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs2229369	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs2240120	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs2240121	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs2240122	1.00[CHB][hapmap];0.82[CHD][hapmap];0.93[JPT][hapmap]
rs2278868	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs2305433	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs2325784	0.83[ASN][1000 genomes]
rs2325804	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2325885	0.90[ASN][1000 genomes]
rs2938483	0.83[ASN][1000 genomes]
rs34980108	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs36071506	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3744346	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs3792692	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs3792694	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs3805370	0.84[CHB][hapmap];0.86[JPT][hapmap]
rs3815472	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3897789	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3897986	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs4793779	0.83[CHB][hapmap];0.81[ASN][1000 genomes]
rs4794447	0.83[CHB][hapmap]
rs4794451	1.00[CHB][hapmap];0.91[CHD][hapmap];0.93[JPT][hapmap]
rs55696440	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6504025	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs6504108	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs67345313	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6847	0.92[CHB][hapmap];0.91[CHD][hapmap];0.93[JPT][hapmap]
rs71356521	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7212202	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs7217496	1.00[CHB][hapmap];0.91[CHD][hapmap];0.93[JPT][hapmap]
rs7220520	0.91[CHD][hapmap];0.80[JPT][hapmap]
rs7220768	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs7222136	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs7223867	0.85[CHB][hapmap];0.93[JPT][hapmap]
rs7224014	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs7224461	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs7225550	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs72825596	0.88[EUR][1000 genomes]
rs72827805	0.85[EUR][1000 genomes]
rs72827806	0.85[EUR][1000 genomes]
rs72827810	0.85[EUR][1000 genomes]
rs741058	0.81[EUR][1000 genomes]
rs757353	0.91[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs758999	0.85[CHB][hapmap];0.80[JPT][hapmap]
rs8065670	1.00[CHB][hapmap];0.91[CHD][hapmap];0.93[JPT][hapmap]
rs8066391	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs8069263	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs8071199	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs8071879	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs8072282	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs8077860	1.00[CHB][hapmap];0.91[CHD][hapmap];0.93[JPT][hapmap]
rs8079616	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs875065	1.00[CHB][hapmap];0.91[CHD][hapmap];0.93[JPT][hapmap]
rs954226	0.81[ASN][1000 genomes]
rs978263	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap]
rs9889470	0.99[ASN][1000 genomes]
rs9899275	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs9899461	1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[JPT][hapmap]
rs9903692	0.88[ASN][1000 genomes]
rs9909933	0.90[ASN][1000 genomes]

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs16954268	TUBG1	cis	parietal	SCAN
rs16954268	HSPB9	cis	parietal	SCAN
rs16954268	CDK5RAP3	cis	parietal	SCAN
rs16954268	CBX1	cis	cerebellum	SCAN
rs16954268	HOXB7	cis	cerebellum	SCAN
rs16954268	CDK5RAP3	cis	cerebellum	SCAN
rs16954268	DHX58	cis	parietal	SCAN

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46306600-46335400	Weak transcription	Thymus	Thymus
2	chr17:46314200-46320200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
3	chr17:46315800-46319600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr17:46315800-46319600	Enhancers	HMEC	breast
5	chr17:46315800-46319800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr17:46315800-46319800	Enhancers	HSMM	muscle
7	chr17:46315800-46319800	Enhancers	Osteobl	bone
8	chr17:46315800-46323000	Enhancers	Primary T helper cells PMA-I stimulated	--
9	chr17:46316400-46319600	Enhancers	NH-A	brain
10	chr17:46316400-46322800	Enhancers	Primary T killer memory cells from peripheral blood	blood
11	chr17:46316400-46324600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr17:46316600-46319800	Enhancers	Fetal Muscle Leg	muscle
13	chr17:46316600-46320200	Enhancers	Fetal Kidney	kidney
14	chr17:46316600-46320600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr17:46317200-46320000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr17:46317200-46320200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr17:46317200-46322600	Enhancers	Fetal Intestine Small	intestine
18	chr17:46317200-46324000	Enhancers	Primary T helper cells fromperipheralblood	blood
19	chr17:46317400-46319800	Enhancers	ES-I3 Cell Line	embryonic stem cell
20	chr17:46317400-46319800	Enhancers	Adipose Nuclei	Adipose
21	chr17:46317400-46319800	Enhancers	Small Intestine	intestine
22	chr17:46317400-46322400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr17:46317400-46322800	Enhancers	Primary T helper naive cells from peripheral blood	blood
24	chr17:46317400-46322800	Enhancers	Fetal Intestine Large	intestine
25	chr17:46317600-46319600	Enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr17:46317600-46319600	Enhancers	Duodenum Smooth Muscle	Duodenum
27	chr17:46317600-46319600	Enhancers	Fetal Lung	lung
28	chr17:46317600-46319800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr17:46317600-46319800	Enhancers	Primary T cells fromperipheralblood	blood
30	chr17:46317600-46319800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr17:46317600-46319800	Enhancers	Fetal Stomach	stomach
32	chr17:46317600-46320400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr17:46317800-46319600	Enhancers	Primary hematopoietic stem cells short term culture	blood
34	chr17:46317800-46319600	Enhancers	Duodenum Mucosa	Duodenum
35	chr17:46317800-46319600	Enhancers	Right Ventricle	heart
36	chr17:46317800-46319600	Enhancers	Skeletal Muscle Male	skeletal muscle
37	chr17:46317800-46319800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
38	chr17:46317800-46319800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr17:46317800-46319800	Enhancers	Psoas Muscle	Psoas
40	chr17:46317800-46319800	Enhancers	NHLF	lung
41	chr17:46317800-46320000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr17:46317800-46320200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr17:46317800-46320600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
44	chr17:46317800-46323000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
45	chr17:46318000-46319600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
46	chr17:46318000-46319600	Enhancers	Monocytes-CD14+_RO01746	blood
47	chr17:46318000-46319800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr17:46318000-46319800	Enhancers	HUES64 Cell Line	embryonic stem cell
49	chr17:46318000-46319800	Enhancers	Left Ventricle	heart
50	chr17:46318000-46319800	Enhancers	Skeletal Muscle Female	skeletal muscle

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