Variant report

Variant	rs8030980
Chromosome Location	chr15:40278192-40278193
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11629915	0.80[EUR][1000 genomes]
rs11631801	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11632930	0.83[CEU][hapmap];0.92[GIH][hapmap];0.90[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11633416	0.84[GIH][hapmap]
rs12442713	0.92[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.83[ASN][1000 genomes]
rs12442731	0.91[CHD][hapmap];0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs1656894	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs16970134	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2291626	0.88[EUR][1000 genomes]
rs28617639	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2898973	0.80[EUR][1000 genomes]
rs2934194	0.87[CEU][hapmap];0.87[GIH][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs552251	0.87[CEU][hapmap];0.86[AMR][1000 genomes]
rs55957853	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56143280	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7166430	0.81[EUR][1000 genomes]
rs7173301	0.84[CHD][hapmap];0.83[JPT][hapmap]
rs7173315	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7175589	0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs72729488	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8030025	0.87[GIH][hapmap]
rs8030640	0.87[CEU][hapmap];0.87[GIH][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8030687	0.86[CEU][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8034362	0.87[CHB][hapmap];0.87[GIH][hapmap];0.83[ASN][1000 genomes]
rs9302104	0.89[AMR][1000 genomes];0.86[EUR][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	nsv530816	chr15:40003136-40586792	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv428635	chr15:40274500-40436293	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs8030980	NOP10	cis	cerebellum	SCAN
rs8030980	EIF2AK4	cis	cerebellum	SCAN
rs8030980	EIF2AK4	Cis_1M	lymphoblastoid	RTeQTL
rs8030980	EIF2AK4	cis	lesional skin	skin_eQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40227400-40283400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr15:40228200-40323800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr15:40236600-40303000	Weak transcription	Small Intestine	intestine
4	chr15:40249000-40304800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr15:40250000-40294800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr15:40250200-40299600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr15:40260800-40303400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr15:40262600-40293800	Weak transcription	Stomach Mucosa	stomach
9	chr15:40266400-40281800	Weak transcription	K562	blood
10	chr15:40267800-40278400	Weak transcription	Primary B cells from cord blood	blood
11	chr15:40269000-40284800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr15:40269000-40293200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr15:40269000-40293200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr15:40269200-40278200	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr15:40269200-40282000	Weak transcription	Esophagus	oesophagus
16	chr15:40269200-40283000	Weak transcription	Psoas Muscle	Psoas
17	chr15:40269400-40281600	Weak transcription	Colonic Mucosa	Colon
18	chr15:40269400-40283000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr15:40269600-40278200	Weak transcription	Fetal Brain Female	brain
20	chr15:40269600-40282400	Weak transcription	Fetal Brain Male	brain
21	chr15:40269600-40295600	Weak transcription	Fetal Heart	heart
22	chr15:40269800-40285400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr15:40270200-40278400	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr15:40270400-40282400	Weak transcription	Primary B cells from peripheral blood	blood
25	chr15:40271000-40278200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr15:40271400-40278400	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr15:40276400-40295600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr15:40277600-40287400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr15:40277600-40288000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr15:40277600-40288000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr15:40277600-40288400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr15:40277600-40294600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
33	chr15:40277600-40303600	Strong transcription	HUES48 Cell Line	embryonic stem cell
34	chr15:40277600-40303800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr15:40277600-40304400	Strong transcription	HUES6 Cell Line	embryonic stem cell
36	chr15:40277800-40278800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr15:40277800-40278800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr15:40277800-40278800	Strong transcription	Gastric	stomach
39	chr15:40277800-40278800	Strong transcription	Spleen	Spleen
40	chr15:40277800-40279000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr15:40277800-40279000	Strong transcription	Thymus	Thymus
42	chr15:40277800-40279400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
43	chr15:40277800-40279400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
44	chr15:40277800-40279400	Strong transcription	Fetal Thymus	thymus
45	chr15:40277800-40279600	Strong transcription	Aorta	Aorta
46	chr15:40277800-40279600	Strong transcription	Brain Angular Gyrus	brain
47	chr15:40277800-40279600	Strong transcription	Brain Hippocampus Middle	brain
48	chr15:40277800-40279600	Strong transcription	Colon Smooth Muscle	Colon
49	chr15:40277800-40279600	Strong transcription	Fetal Lung	lung
50	chr15:40277800-40279600	Strong transcription	Placenta Amnion	Placenta Amnion

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