Variant report

Variant	rs852978
Chromosome Location	chr5:142690596-142690597
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	chr5:142677715..142680053-chr5:142689105..142691252,2	K562	blood:

Extended variants
information (count: 73 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10052957	1.00[JPT][hapmap]
rs10482614	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10515522	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];0.87[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];0.94[YRI][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1635475	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs174048	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs174050	0.97[AMR][1000 genomes];0.97[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	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs258750	1.00[JPT][hapmap]
rs258751	1.00[ASN][1000 genomes]
rs258752	0.81[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	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];0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[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];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2918419	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]
rs2963148	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2963149	1.00[JPT][hapmap]
rs2963150	0.95[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[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];0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs33380	0.95[ASN][1000 genomes]
rs33381	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs33382	0.99[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[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];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41423247	0.83[AFR][1000 genomes]
rs55817235	0.87[EUR][1000 genomes]
rs56150733	0.87[EUR][1000 genomes]
rs61752263	0.86[EUR][1000 genomes]
rs6188	1.00[JPT][hapmap]
rs6194	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[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];0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[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];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72801029	0.80[EUR][1000 genomes]
rs72801054	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72801080	0.86[EUR][1000 genomes]
rs72801090	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72801096	0.84[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs852977	1.00[JPT][hapmap]
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	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs853154	0.82[EUR][1000 genomes]
rs853156	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs853157	1.00[CHB][hapmap];0.85[JPT][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs853176	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs853177	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs853178	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs853179	0.81[AMR][1000 genomes];0.86[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];0.81[AMR][1000 genomes];0.97[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	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs860465	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs862489	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs864082	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs864355	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs865482	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[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];0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[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	esv33748	chr5:142638267-142699595	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
3	nsv5041	chr5:142653189-142697896	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs852978	STK32A	cis	cerebellum	SCAN

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:142655800-142699200	Strong transcription	Dnd41	blood
2	chr5:142657800-142695400	Weak transcription	Pancreas	Pancrea
3	chr5:142658200-142694800	Weak transcription	Right Ventricle	heart
4	chr5:142658400-142714800	Weak transcription	Esophagus	oesophagus
5	chr5:142659800-142692600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr5:142664400-142693400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr5:142668800-142693800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr5:142677600-142697800	Weak transcription	Fetal Brain Male	brain
9	chr5:142678200-142695400	Weak transcription	Gastric	stomach
10	chr5:142678400-142691400	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr5:142678400-142693400	Weak transcription	Aorta	Aorta
12	chr5:142678400-142693400	Weak transcription	Rectal Smooth Muscle	rectum
13	chr5:142678400-142693600	Weak transcription	Brain Angular Gyrus	brain
14	chr5:142678400-142693800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr5:142680200-142691000	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr5:142680200-142691400	Weak transcription	Ovary	ovary
17	chr5:142680200-142691600	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr5:142680200-142691800	Weak transcription	Brain Substantia Nigra	brain
19	chr5:142680400-142690800	Weak transcription	HepG2	liver
20	chr5:142682000-142691200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr5:142682600-142698400	Weak transcription	Stomach Mucosa	stomach
22	chr5:142682800-142691400	Strong transcription	Primary T helper cells PMA-I stimulated	--
23	chr5:142683200-142693800	Strong transcription	Primary T cells from cord blood	blood
24	chr5:142683200-142693800	Strong transcription	Fetal Muscle Trunk	muscle
25	chr5:142683200-142693800	Strong transcription	Fetal Thymus	thymus
26	chr5:142683400-142693000	Strong transcription	Primary B cells from peripheral blood	blood
27	chr5:142684000-142690800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr5:142684200-142693200	Strong transcription	Liver	Liver
29	chr5:142684200-142697800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr5:142684400-142693200	Strong transcription	Adipose Nuclei	Adipose
31	chr5:142684400-142693600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr5:142684600-142691200	Strong transcription	HSMM	muscle
33	chr5:142685000-142692600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr5:142685000-142693600	Strong transcription	Fetal Intestine Large	intestine
35	chr5:142685000-142694000	Strong transcription	Primary T helper cells fromperipheralblood	blood
36	chr5:142685400-142690600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr5:142685400-142691400	Weak transcription	Brain Anterior Caudate	brain
38	chr5:142685400-142691600	Weak transcription	Brain Hippocampus Middle	brain
39	chr5:142685400-142691800	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr5:142685400-142692200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr5:142685400-142692400	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr5:142685400-142693400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr5:142685600-142692600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr5:142686000-142690800	Strong transcription	Osteobl	bone
45	chr5:142686000-142691600	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr5:142686000-142693400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr5:142686200-142690600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr5:142686200-142693200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr5:142686400-142691800	Strong transcription	Fetal Intestine Small	intestine
50	chr5:142686600-142692000	Strong transcription	Fetal Stomach	stomach

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