Variant report

Variant	rs17272754
Chromosome Location	chr3:16984414-16984415
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:16977790..16979342-chr3:16983093..16986070,2	K562	blood:

Extended variants
information (count: 44 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs11549706	0.85[TSI][hapmap]
rs12054464	0.90[EUR][1000 genomes]
rs12233538	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs12233541	0.88[EUR][1000 genomes]
rs13062572	0.84[TSI][hapmap]
rs13073804	1.00[CEU][hapmap];1.00[CHD][hapmap];0.96[TSI][hapmap];0.95[EUR][1000 genomes]
rs13085309	0.88[TSI][hapmap]
rs13089569	0.85[TSI][hapmap]
rs1550518	0.95[EUR][1000 genomes]
rs17042926	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs17200543	1.00[CEU][hapmap];1.00[CHD][hapmap];0.96[TSI][hapmap];0.97[EUR][1000 genomes]
rs17272740	0.97[EUR][1000 genomes]
rs17272810	0.82[CEU][hapmap];1.00[CHD][hapmap];0.92[TSI][hapmap]
rs17272831	0.82[CEU][hapmap];1.00[CHD][hapmap];0.92[TSI][hapmap]
rs28498854	0.95[ASN][1000 genomes]
rs34053933	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34126040	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34437014	0.92[EUR][1000 genomes]
rs35307172	0.93[EUR][1000 genomes]
rs35941157	0.98[ASN][1000 genomes]
rs3935970	0.82[CEU][hapmap];1.00[CHD][hapmap];0.92[TSI][hapmap]
rs4130495	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs55942882	0.93[EUR][1000 genomes]
rs58855245	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59256854	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62246031	0.93[EUR][1000 genomes]
rs6442659	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6769249	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6775782	0.88[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6778233	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6789069	0.88[CEU][hapmap];1.00[CHD][hapmap];0.92[TSI][hapmap]
rs6796868	0.88[CHD][hapmap]
rs6805550	0.98[ASN][1000 genomes]
rs7616589	0.81[CEU][hapmap]
rs7645276	0.98[ASN][1000 genomes]
rs7652293	0.82[CEU][hapmap];1.00[CHD][hapmap];0.92[TSI][hapmap]
rs9815788	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs9834723	0.80[CEU][hapmap]
rs9835432	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9845137	0.82[CEU][hapmap]
rs9845551	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9870977	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9876768	0.82[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.96[TSI][hapmap];0.95[ASN][1000 genomes]
rs9881997	0.98[ASN][1000 genomes]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17272754	TMEM43	cis	cerebellum	SCAN
rs17272754	PLCL2	cis	Whole Blood	GTEx
rs17272754	SGOL1	cis	cerebellum	SCAN
rs17272754	COLQ	cis	parietal	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:16959400-16986600	Weak transcription	Aorta	Aorta
2	chr3:16967000-16985000	Enhancers	Primary T helper cells fromperipheralblood	blood
3	chr3:16973800-16985000	Enhancers	Primary T helper naive cells from peripheral blood	blood
4	chr3:16974800-16984800	Weak transcription	Stomach Mucosa	stomach
5	chr3:16975600-16985000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr3:16975600-16985800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
7	chr3:16975800-16985000	Enhancers	Primary T killer memory cells from peripheral blood	blood
8	chr3:16977800-16987400	Enhancers	Primary T helper cells PMA-I stimulated	--
9	chr3:16978000-16985800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
10	chr3:16978000-16991200	Weak transcription	Adipose Nuclei	Adipose
11	chr3:16979000-16990600	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr3:16979400-16985000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr3:16979400-16989800	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr3:16980000-16985000	Enhancers	Primary hematopoietic stem cells	blood
15	chr3:16980400-16985800	Weak transcription	GM12878-XiMat	blood
16	chr3:16981200-16985600	Enhancers	Primary T cells from cord blood	blood
17	chr3:16981400-16986000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr3:16981600-16985000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
19	chr3:16982400-16984800	Enhancers	Fetal Lung	lung
20	chr3:16983000-16984800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr3:16983000-16988600	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr3:16983200-16984800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr3:16983200-16985400	Weak transcription	Ovary	ovary
24	chr3:16983200-16985800	Weak transcription	Fetal Intestine Large	intestine
25	chr3:16983200-16985800	Weak transcription	Fetal Intestine Small	intestine
26	chr3:16983400-16987600	Enhancers	Fetal Heart	heart
27	chr3:16983600-16984600	Enhancers	Primary B cells from cord blood	blood
28	chr3:16983600-16985000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
29	chr3:16983600-16985000	Enhancers	Brain Angular Gyrus	brain
30	chr3:16983800-16984800	Enhancers	Primary hematopoietic stem cells short term culture	blood
31	chr3:16983800-16985000	Enhancers	Small Intestine	intestine
32	chr3:16983800-16986000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr3:16984000-16984600	Enhancers	Fetal Brain Female	brain
34	chr3:16984000-16985000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr3:16984000-16985800	Weak transcription	Right Atrium	heart
36	chr3:16984000-16985800	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr3:16984000-16987200	Weak transcription	Right Ventricle	heart
38	chr3:16984000-16992600	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr3:16984200-16985800	Weak transcription	Left Ventricle	heart
40	chr3:16984200-16986400	Weak transcription	Psoas Muscle	Psoas
41	chr3:16984200-17003400	Weak transcription	Spleen	Spleen
42	chr3:16984400-16984800	Weak transcription	Primary T cells fromperipheralblood	blood
43	chr3:16984400-16984800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr3:16984400-16985800	Weak transcription	Primary B cells from peripheral blood	blood
45	chr3:16984400-16987400	Weak transcription	Pancreatic Islets	Pancreatic Islet

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