Variant report

Variant	rs33389
Chromosome Location	chr5:142700499-142700500
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	chr5:142694144..142696912-chr5:142699243..142701777,2	K562	blood:

Extended variants
information (count: 70 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10052957	1.00[JPT][hapmap]
rs10482614	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10515522	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];0.86[EUR][1000 genomes]
rs11747997	0.91[ASN][1000 genomes]
rs11749561	1.00[JPT][hapmap]
rs1438732	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1635475	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs174048	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs174050	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1837262	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1866388	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs190488	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2043840	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs258748	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs258750	1.00[JPT][hapmap]
rs258751	1.00[ASN][1000 genomes]
rs258752	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs258753	0.85[JPT][hapmap]
rs258757	0.82[ASN][1000 genomes]
rs258813	1.00[JPT][hapmap]
rs258814	1.00[ASN][1000 genomes]
rs2918415	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];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2918416	1.00[JPT][hapmap]
rs2918417	1.00[JPT][hapmap]
rs2918418	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2918419	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];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2963148	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2963149	1.00[JPT][hapmap]
rs2963150	0.95[ASN][1000 genomes]
rs2963151	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2963154	0.94[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];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs33380	0.95[ASN][1000 genomes]
rs33381	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs33382	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55817235	0.86[EUR][1000 genomes]
rs56150733	0.86[EUR][1000 genomes]
rs61752263	0.87[EUR][1000 genomes]
rs6188	1.00[JPT][hapmap]
rs6194	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6196	0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6861962	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs712189	1.00[CHB][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72801054	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72801080	0.87[EUR][1000 genomes]
rs72801090	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72801096	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs852977	1.00[JPT][hapmap]
rs852978	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];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs852979	0.98[ASN][1000 genomes]
rs852982	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs852984	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs853154	0.81[EUR][1000 genomes]
rs853156	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs853157	1.00[CHB][hapmap];0.85[JPT][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs853176	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs853177	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs853178	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs853179	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs853182	1.00[ASN][1000 genomes]
rs853184	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs860457	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs860458	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs860465	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs862489	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs864082	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs864355	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs865482	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9324918	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1825941	chr5:142568715-142728031	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv1023976	chr5:142692062-142813664	Enhancers Flanking Active TSS Genic enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs33389	STK32A	cis	cerebellum	SCAN

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:142658400-142714800	Weak transcription	Esophagus	oesophagus
2	chr5:142689000-142707600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr5:142691600-142703400	Weak transcription	Spleen	Spleen
4	chr5:142692200-142702600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr5:142692400-142710600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr5:142692600-142707000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr5:142693000-142707200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr5:142693200-142702200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr5:142693200-142714400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr5:142693400-142721000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr5:142693600-142705200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr5:142693600-142706600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr5:142693800-142701800	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr5:142693800-142702000	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr5:142693800-142702200	Weak transcription	Primary T cells from cord blood	blood
16	chr5:142693800-142702400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr5:142693800-142702600	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr5:142693800-142703600	Weak transcription	Thymus	Thymus
19	chr5:142693800-142703800	Weak transcription	Fetal Thymus	thymus
20	chr5:142693800-142707200	Weak transcription	Fetal Stomach	stomach
21	chr5:142693800-142747400	Weak transcription	Fetal Muscle Trunk	muscle
22	chr5:142694000-142701800	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr5:142695000-142703400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr5:142695800-142703800	Weak transcription	Fetal Muscle Leg	muscle
25	chr5:142696200-142702600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr5:142696200-142703000	Weak transcription	Lung	lung
27	chr5:142696200-142704000	Weak transcription	Primary B cells from peripheral blood	blood
28	chr5:142696400-142708200	Weak transcription	Colon Smooth Muscle	Colon
29	chr5:142696600-142700600	Weak transcription	GM12878-XiMat	blood
30	chr5:142696600-142702400	Weak transcription	NH-A	brain
31	chr5:142696800-142702000	Weak transcription	HSMMtube	muscle
32	chr5:142697000-142702200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr5:142697000-142702800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
34	chr5:142697000-142705800	Weak transcription	Rectal Smooth Muscle	rectum
35	chr5:142697200-142701400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr5:142697200-142704400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr5:142697200-142714600	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr5:142697200-142720400	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr5:142697400-142707400	Weak transcription	Ovary	ovary
40	chr5:142697600-142700800	Weak transcription	Primary B cells from cord blood	blood
41	chr5:142697600-142702400	Weak transcription	HSMM	muscle
42	chr5:142697600-142703600	Weak transcription	Right Ventricle	heart
43	chr5:142697600-142707200	Weak transcription	Placenta	Placenta
44	chr5:142697800-142703400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr5:142697800-142703600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr5:142697800-142711400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr5:142698200-142701400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr5:142698200-142709200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr5:142698600-142703600	Weak transcription	Primary hematopoietic stem cells	blood
50	chr5:142698800-142701200	Enhancers	Fetal Heart	heart

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