Variant report

Variant	rs12542457
Chromosome Location	chr8:9564600-9564601
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 85 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10094989	0.95[CEU][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10099122	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10102170	0.95[CEU][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10104032	0.83[CEU][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10106040	0.83[CEU][hapmap];0.88[EUR][1000 genomes]
rs10109026	0.86[JPT][hapmap]
rs10111376	0.83[CEU][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10903317	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11249934	0.95[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap]
rs11249939	0.89[ASN][1000 genomes]
rs11776236	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs11778555	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11779335	0.85[LWK][hapmap];0.93[MKK][hapmap]
rs11782886	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11785458	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11785923	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12114182	0.84[AFR][1000 genomes]
rs12114661	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12155819	0.89[ASW][hapmap];1.00[CEU][hapmap];0.88[GIH][hapmap];0.94[LWK][hapmap];0.87[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.80[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12541617	0.84[AFR][1000 genomes]
rs12542912	1.00[CEU][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12543959	0.84[AFR][1000 genomes]
rs12544371	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs12545250	0.91[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs12545912	0.83[MKK][hapmap]
rs12547642	0.83[EUR][1000 genomes]
rs12677313	0.82[AFR][1000 genomes]
rs12677507	0.94[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs12679180	0.82[AFR][1000 genomes]
rs12679956	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12682175	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs13250951	0.81[AMR][1000 genomes]
rs13260526	0.81[AFR][1000 genomes]
rs13264850	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13272424	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13276086	0.83[ASW][hapmap];0.91[CEU][hapmap];0.88[GIH][hapmap];0.96[LWK][hapmap];0.87[MEX][hapmap];0.97[MKK][hapmap];0.92[TSI][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13282006	0.81[AFR][1000 genomes]
rs1394	0.95[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs33994795	0.83[EUR][1000 genomes]
rs35316422	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35874762	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4075359	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs4128198	0.91[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap]
rs4129360	1.00[CEU][hapmap];0.80[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4313162	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs4422774	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4554469	0.81[ASN][1000 genomes]
rs4612345	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4840426	0.89[ASW][hapmap];0.82[CEU][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap]
rs4840437	0.89[ASW][hapmap];0.83[CEU][hapmap];0.94[LWK][hapmap];0.83[MEX][hapmap];0.96[MKK][hapmap];0.94[TSI][hapmap];0.80[YRI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4841196	0.95[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.89[MKK][hapmap];0.93[YRI][hapmap];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4841203	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4841204	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4841212	0.81[MKK][hapmap]
rs6601327	0.82[MKK][hapmap]
rs6601338	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs6601340	0.95[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs6601344	0.82[AFR][1000 genomes]
rs6601350	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs67711814	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6982148	1.00[CEU][hapmap];0.80[YRI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6989782	0.87[MEX][hapmap]
rs6990300	0.82[ASW][hapmap];0.88[GIH][hapmap];0.93[LWK][hapmap];0.94[MKK][hapmap];0.82[AFR][1000 genomes]
rs6990418	0.91[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap]
rs6992666	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6994574	1.00[CEU][hapmap];0.88[GIH][hapmap];0.87[LWK][hapmap];0.87[MEX][hapmap];0.96[MKK][hapmap];0.94[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6995495	0.82[YRI][hapmap]
rs7001832	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7003791	0.85[CEU][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs7004937	0.91[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap]
rs7006985	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7009721	0.87[MEX][hapmap]
rs7014663	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73202879	0.80[ASN][1000 genomes]
rs7459728	0.87[MEX][hapmap]
rs7461939	1.00[CEU][hapmap];0.88[GIH][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.94[TSI][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7462070	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7462910	0.85[LWK][hapmap];0.93[MKK][hapmap]
rs7822700	0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs7846399	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9644704	0.83[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9644707	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9650639	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs9657509	0.80[AMR][1000 genomes];0.85[EUR][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	nsv530864	chr8:9097498-9914548	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs12542457	PRSS55	cis	cerebellum	SCAN
rs12542457	MFHAS1	cis	cerebellum	SCAN
rs12542457	CLDN23	cis	multi-tissue	Pritchard
rs12542457	DEFB134	cis	cerebellum	SCAN
rs12542457	C8orf79	cis	parietal	SCAN
rs12542457	TNKS	cis	parietal	SCAN
rs12542457	FLJ10661	cis	cerebellum	SCAN
rs12542457	PPP1R3B	cis	lymphoblastoid	seeQTL
rs12542457	C8orf13	cis	multi-tissue	Pritchard

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:9513200-9567400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr8:9513400-9605400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr8:9529600-9606400	Weak transcription	Esophagus	oesophagus
4	chr8:9535000-9564800	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr8:9535000-9608000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr8:9537600-9592400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr8:9540000-9565400	Weak transcription	Fetal Kidney	kidney
8	chr8:9541400-9592200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr8:9542200-9606800	Weak transcription	Small Intestine	intestine
10	chr8:9543000-9592200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr8:9543400-9606400	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr8:9544000-9586200	Weak transcription	Thymus	Thymus
13	chr8:9544000-9592400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr8:9544000-9592400	Weak transcription	Psoas Muscle	Psoas
15	chr8:9544200-9571200	Weak transcription	Aorta	Aorta
16	chr8:9545600-9568600	Weak transcription	HSMMtube	muscle
17	chr8:9545600-9592400	Weak transcription	Brain Angular Gyrus	brain
18	chr8:9548000-9570600	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr8:9548400-9584400	Weak transcription	Hela-S3	cervix
20	chr8:9549000-9567200	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr8:9550000-9627600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr8:9551000-9592400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr8:9551200-9610600	Weak transcription	Fetal Brain Male	brain
24	chr8:9554600-9567200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr8:9554600-9567200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr8:9554800-9575600	Weak transcription	Fetal Heart	heart
27	chr8:9555400-9586400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr8:9555600-9567000	Weak transcription	Fetal Lung	lung
29	chr8:9556800-9569600	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr8:9557400-9632200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr8:9558000-9564600	Weak transcription	Rectal Smooth Muscle	rectum
32	chr8:9558000-9592400	Weak transcription	Gastric	stomach
33	chr8:9558400-9597600	Weak transcription	Spleen	Spleen
34	chr8:9558400-9605000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr8:9559400-9567000	Weak transcription	Brain Hippocampus Middle	brain
36	chr8:9559400-9592400	Weak transcription	Right Ventricle	heart
37	chr8:9560600-9564800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr8:9560600-9609200	Weak transcription	K562	blood
39	chr8:9561000-9565000	Weak transcription	Primary neutrophils fromperipheralblood	blood
40	chr8:9561000-9567400	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr8:9561000-9616200	Weak transcription	Brain Substantia Nigra	brain
42	chr8:9561200-9576800	Weak transcription	GM12878-XiMat	blood
43	chr8:9561400-9565400	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr8:9561400-9592000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr8:9562000-9569800	Strong transcription	Primary T helper cells PMA-I stimulated	--
46	chr8:9562000-9572800	Strong transcription	Monocytes-CD14+_RO01746	blood
47	chr8:9562000-9574400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr8:9562200-9565400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr8:9562200-9569800	Strong transcription	Primary monocytes fromperipheralblood	blood
50	chr8:9562200-9577800	Weak transcription	Lung	lung

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