Variant report

Variant	rs2918419
Chromosome Location	chr5:142722353-142722354
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:142719538..142722482-chr5:142727185..142728885,2	K562	blood:

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

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10052957	1.00[JPT][hapmap]
rs10482614	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10515522	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];0.90[EUR][1000 genomes]
rs11747997	0.95[ASN][1000 genomes]
rs11749561	1.00[JPT][hapmap]
rs1438732	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1635475	0.80[ASN][1000 genomes]
rs174048	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs174050	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1837262	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1866388	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs190488	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2043840	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs258748	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs258750	1.00[JPT][hapmap]
rs258751	0.95[ASN][1000 genomes]
rs258752	0.80[ASN][1000 genomes]
rs258753	0.85[JPT][hapmap]
rs258813	1.00[JPT][hapmap]
rs258814	0.95[ASN][1000 genomes]
rs2918415	0.92[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];0.94[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[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];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2963148	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2963149	1.00[JPT][hapmap]
rs2963150	1.00[ASN][1000 genomes]
rs2963151	1.00[ASW][hapmap];1.00[CEU][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];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2963154	0.92[ASW][hapmap];0.94[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];0.94[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs33380	1.00[ASN][1000 genomes]
rs33381	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs33382	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs33389	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]
rs41423247	0.81[AFR][1000 genomes]
rs55817235	0.90[EUR][1000 genomes]
rs56150733	0.90[EUR][1000 genomes]
rs61752263	0.91[EUR][1000 genomes]
rs6188	1.00[JPT][hapmap]
rs6194	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6196	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6861962	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs712189	1.00[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs72801054	0.92[EUR][1000 genomes]
rs72801080	0.91[EUR][1000 genomes]
rs72801090	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72801096	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs852977	1.00[JPT][hapmap]
rs852978	1.00[ASW][hapmap];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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs852979	0.93[ASN][1000 genomes]
rs852982	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs852984	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs853156	0.80[ASN][1000 genomes]
rs853157	1.00[CHB][hapmap];0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs853176	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs853177	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs853178	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs853179	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs853182	0.95[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];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs860457	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs860458	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs860465	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs862489	0.81[AMR][1000 genomes]
rs864082	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs864355	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs865482	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9324918	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.89[TSI][hapmap];0.94[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	nsv1033408	chr5:142701353-142738882	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2918419	STK32A	cis	cerebellum	SCAN

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:142693800-142747400	Weak transcription	Fetal Muscle Trunk	muscle
2	chr5:142702000-142725800	Weak transcription	Aorta	Aorta
3	chr5:142703000-142727200	Weak transcription	HSMM	muscle
4	chr5:142704200-142728800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr5:142705200-142725600	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr5:142705800-142722400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr5:142707400-142734800	Weak transcription	Placenta	Placenta
8	chr5:142707800-142727400	Weak transcription	Fetal Muscle Leg	muscle
9	chr5:142708000-142724400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr5:142708000-142727200	Weak transcription	Fetal Thymus	thymus
11	chr5:142708000-142727400	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr5:142708000-142728800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr5:142708000-142735400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr5:142708000-142735400	Weak transcription	Fetal Stomach	stomach
15	chr5:142708600-142724400	Weak transcription	Fetal Intestine Small	intestine
16	chr5:142708800-142726400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr5:142709000-142725600	Weak transcription	Primary B cells from peripheral blood	blood
18	chr5:142709000-142725800	Weak transcription	Primary T cells from cord blood	blood
19	chr5:142709200-142725600	Weak transcription	Duodenum Mucosa	Duodenum
20	chr5:142711800-142728600	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr5:142714800-142726200	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr5:142715200-142726600	Weak transcription	HepG2	liver
23	chr5:142716000-142730200	Weak transcription	Fetal Lung	lung
24	chr5:142716400-142726400	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr5:142716600-142734200	Weak transcription	Ovary	ovary
26	chr5:142717000-142725600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr5:142718800-142725800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr5:142719200-142726400	Weak transcription	Primary hematopoietic stem cells	blood
29	chr5:142719400-142725000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr5:142719400-142725800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr5:142719400-142735400	Weak transcription	Gastric	stomach
32	chr5:142720400-142722400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr5:142720400-142722400	Enhancers	Liver	Liver
34	chr5:142720400-142722800	Enhancers	Brain Anterior Caudate	brain
35	chr5:142720400-142722800	Enhancers	Skeletal Muscle Male	skeletal muscle
36	chr5:142720400-142723200	Enhancers	Fetal Heart	heart
37	chr5:142720400-142723200	Genic enhancers	A549	lung
38	chr5:142720400-142723400	Enhancers	Colon Smooth Muscle	Colon
39	chr5:142720600-142722400	Enhancers	Hela-S3	cervix
40	chr5:142720600-142722600	Weak transcription	Left Ventricle	heart
41	chr5:142720600-142723000	Enhancers	NHLF	lung
42	chr5:142720600-142723200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr5:142720600-142723200	Enhancers	Brain Cingulate Gyrus	brain
44	chr5:142720600-142723200	Enhancers	Brain Hippocampus Middle	brain
45	chr5:142720600-142723200	Enhancers	NHDF-Ad	bronchial
46	chr5:142720600-142723600	Enhancers	Primary T helper cells PMA-I stimulated	--
47	chr5:142720600-142725600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr5:142720800-142722400	Enhancers	GM12878-XiMat	blood
49	chr5:142720800-142723000	Enhancers	Skeletal Muscle Female	skeletal muscle
50	chr5:142720800-142723200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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