Variant report

Variant	rs17200543
Chromosome Location	chr3:16973762-16973763
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs11549706	0.89[TSI][hapmap]
rs12054464	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12233538	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12233541	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13062572	0.87[TSI][hapmap]
rs13073804	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13083189	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs13085309	0.92[TSI][hapmap]
rs13089569	0.89[TSI][hapmap]
rs13096536	1.00[JPT][hapmap]
rs1550518	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17042926	0.88[CHD][hapmap]
rs17042972	0.81[ASN][1000 genomes]
rs17272740	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17272754	1.00[CEU][hapmap];1.00[CHD][hapmap];0.96[TSI][hapmap];0.97[EUR][1000 genomes]
rs17272810	0.82[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.81[AMR][1000 genomes]
rs17272817	0.86[AMR][1000 genomes]
rs17272831	0.82[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.96[TSI][hapmap];0.86[AMR][1000 genomes]
rs34053933	0.88[EUR][1000 genomes]
rs34126040	0.94[EUR][1000 genomes]
rs34437014	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34824028	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35307172	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3935970	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.96[TSI][hapmap];0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4290789	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55942882	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56060350	0.86[AMR][1000 genomes]
rs58855245	0.88[EUR][1000 genomes]
rs59256854	0.88[EUR][1000 genomes]
rs62246031	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62247182	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6789069	0.88[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.83[AMR][1000 genomes]
rs6796868	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7616589	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7652293	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.96[TSI][hapmap];0.86[AMR][1000 genomes]
rs9815788	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9834723	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9835432	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs9845137	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9858664	0.85[ASN][1000 genomes]
rs9876768	0.82[CEU][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];0.92[TSI][hapmap]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17200543	SATB1	cis	parietal	SCAN
rs17200543	TMEM43	cis	cerebellum	SCAN
rs17200543	COLQ	cis	parietal	SCAN
rs17200543	SGOL1	cis	cerebellum	SCAN

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:16958000-16981800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr3:16959400-16986600	Weak transcription	Aorta	Aorta
3	chr3:16965000-16979000	Weak transcription	Lung	lung
4	chr3:16967000-16985000	Enhancers	Primary T helper cells fromperipheralblood	blood
5	chr3:16967600-16977200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr3:16967800-16977800	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr3:16968800-16974000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr3:16969000-16974000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr3:16969000-16977400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
10	chr3:16969600-16977400	Weak transcription	Fetal Thymus	thymus
11	chr3:16970000-16977000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr3:16970200-16974200	Weak transcription	Primary hematopoietic stem cells	blood
13	chr3:16970200-16974600	Weak transcription	Gastric	stomach
14	chr3:16970200-16975600	Weak transcription	Pancreas	Pancrea
15	chr3:16970400-16977400	Weak transcription	Thymus	Thymus
16	chr3:16970800-16977000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr3:16971400-16974000	Weak transcription	Stomach Mucosa	stomach
18	chr3:16971400-16974200	Weak transcription	Primary monocytes fromperipheralblood	blood
19	chr3:16971400-16975600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr3:16971600-16974000	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr3:16971600-16974600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr3:16971600-16974600	Weak transcription	Left Ventricle	heart
23	chr3:16971600-16975600	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr3:16971600-16975600	Weak transcription	Adipose Nuclei	Adipose
25	chr3:16971600-16975600	Weak transcription	Spleen	Spleen
26	chr3:16971600-16982400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr3:16971800-16974200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr3:16972000-16977600	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr3:16972200-16974600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr3:16972200-16977200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr3:16972400-16973800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr3:16972400-16974600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr3:16972400-16975600	Weak transcription	Psoas Muscle	Psoas
34	chr3:16972400-16983600	Weak transcription	Brain Angular Gyrus	brain
35	chr3:16972600-16973800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr3:16972600-16974200	Weak transcription	Primary T cells from cord blood	blood
37	chr3:16972600-16974200	Weak transcription	Ovary	ovary
38	chr3:16972600-16974200	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr3:16972600-16974400	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr3:16972600-16975600	Weak transcription	Right Ventricle	heart
41	chr3:16972600-16975800	Weak transcription	Right Atrium	heart
42	chr3:16973000-16974000	ZNF genes & repeats	GM12878-XiMat	blood
43	chr3:16973000-16976400	Strong transcription	Primary B cells from cord blood	blood
44	chr3:16973200-16974600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
45	chr3:16973400-16973800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
46	chr3:16973400-16980400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
47	chr3:16973600-16974000	Weak transcription	Primary B cells from peripheral blood	blood
48	chr3:16973600-16974200	Weak transcription	Fetal Heart	heart
49	chr3:16973600-16977000	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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