Variant report

Variant	rs2963154
Chromosome Location	chr5:142742537-142742538
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	chr5:142712062..142716024-chr5:142739998..142742842,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000231579	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10052957	1.00[JPT][hapmap]
rs10482614	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10515522	0.94[CEU][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11747997	0.95[ASN][1000 genomes]
rs11749561	1.00[JPT][hapmap]
rs1438732	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1635475	0.80[ASN][1000 genomes]
rs174048	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs174050	0.84[AMR][1000 genomes];0.86[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	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[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	1.00[ASW][hapmap];0.94[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];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2918416	1.00[JPT][hapmap]
rs2918417	1.00[JPT][hapmap]
rs2918418	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2918419	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]
rs2963148	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2963149	1.00[JPT][hapmap]
rs2963150	1.00[ASN][1000 genomes]
rs2963151	0.92[ASW][hapmap];0.94[CEU][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];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs33380	1.00[ASN][1000 genomes]
rs33381	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs33382	0.93[AFR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs33389	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]
rs41423247	0.85[AFR][1000 genomes]
rs55817235	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56150733	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61752263	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6188	1.00[JPT][hapmap]
rs6194	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6196	0.92[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.94[TSI][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];0.84[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	0.86[EUR][1000 genomes]
rs72801080	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72801090	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72801096	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs852977	1.00[JPT][hapmap]
rs852978	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];0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[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	0.87[AMR][1000 genomes];0.89[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	0.80[ASN][1000 genomes]
rs853179	0.83[ASN][1000 genomes]
rs853182	0.95[ASN][1000 genomes]
rs853184	0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.86[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	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs864082	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs864355	0.83[ASN][1000 genomes]
rs865482	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9324918	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
rs2963154	STK32A	cis	cerebellum	SCAN

Chromatin state (count:77 , 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	chr5:142725000-142764200	Weak transcription	Lung	lung
3	chr5:142734000-142743000	Enhancers	Primary T helper naive cells from peripheral blood	blood
4	chr5:142734000-142756400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr5:142734200-142743600	Enhancers	Primary T helper cells PMA-I stimulated	--
6	chr5:142734200-142743600	Enhancers	Primary T helper cells fromperipheralblood	blood
7	chr5:142734200-142754200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr5:142735600-142743000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr5:142735600-142743600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr5:142735600-142743600	Weak transcription	HSMM	muscle
11	chr5:142735600-142743800	Weak transcription	Primary hematopoietic stem cells	blood
12	chr5:142735600-142756000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr5:142735800-142748200	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr5:142735800-142751200	Weak transcription	HMEC	breast
15	chr5:142735800-142751800	Weak transcription	NHEK	skin
16	chr5:142736200-142746200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr5:142736200-142748200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr5:142736200-142755800	Weak transcription	Small Intestine	intestine
19	chr5:142736200-142756000	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr5:142736800-142746800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr5:142737000-142745200	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr5:142737200-142742600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr5:142738400-142742800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr5:142738800-142744000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
25	chr5:142739400-142763600	Weak transcription	Thymus	Thymus
26	chr5:142739600-142754200	Weak transcription	Fetal Thymus	thymus
27	chr5:142739800-142743400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr5:142739800-142743600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
29	chr5:142740000-142742600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr5:142740000-142742600	Enhancers	Adipose Nuclei	Adipose
31	chr5:142740000-142742600	Enhancers	Fetal Heart	heart
32	chr5:142740000-142743200	Enhancers	HepG2	liver
33	chr5:142740200-142742600	Enhancers	Primary B cells from peripheral blood	blood
34	chr5:142740400-142743000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr5:142740600-142743600	Weak transcription	NHDF-Ad	bronchial
36	chr5:142740600-142752600	Weak transcription	Colon Smooth Muscle	Colon
37	chr5:142740600-142755800	Weak transcription	Right Ventricle	heart
38	chr5:142740800-142743400	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr5:142740800-142743600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr5:142740800-142745200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr5:142740800-142747200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr5:142740800-142752600	Weak transcription	Rectal Smooth Muscle	rectum
43	chr5:142741000-142743200	Enhancers	Psoas Muscle	Psoas
44	chr5:142741200-142742600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr5:142741200-142743000	Enhancers	K562	blood
46	chr5:142741200-142743400	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr5:142741200-142743400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr5:142741200-142743400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr5:142741200-142743600	Weak transcription	NHLF	lung
50	chr5:142741200-142748800	Weak transcription	Skeletal Muscle Female	skeletal muscle

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