Variant report

Variant	rs10454066
Chromosome Location	chr16:69699005-69699006
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 103 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs10048108	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10163235	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10500551	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10852457	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10852458	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11075727	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11075728	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11075730	0.95[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11075733	0.85[EUR][1000 genomes]
rs11075734	1.00[CEU][hapmap];0.95[GIH][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes]
rs1139178	0.85[EUR][1000 genomes]
rs11639947	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];0.95[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11641050	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11641233	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11641521	0.80[EUR][1000 genomes]
rs11642030	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11642115	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11643240	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11643530	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11643926	0.83[EUR][1000 genomes]
rs11644838	0.80[EUR][1000 genomes]
rs11646884	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12232410	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12447326	0.95[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12447883	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12449005	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12595869	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];0.95[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12595878	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12595927	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12596679	1.00[CEU][hapmap];0.95[GIH][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.80[EUR][1000 genomes]
rs12596823	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12925371	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13337236	0.98[ASN][1000 genomes]
rs1437135	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1437136	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16958970	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];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16959025	1.00[CEU][hapmap];0.93[GIH][hapmap];0.94[TSI][hapmap];0.95[EUR][1000 genomes]
rs16959035	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1800566	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];0.95[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1865965	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2118220	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2161631	1.00[CEU][hapmap];0.81[JPT][hapmap]
rs2196574	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2217950	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2361838	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2361839	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3169315	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3743673	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3885612	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4078387	0.80[EUR][1000 genomes]
rs4464069	1.00[CEU][hapmap];0.95[GIH][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.80[EUR][1000 genomes]
rs4497676	1.00[CEU][hapmap]
rs4580150	0.80[EUR][1000 genomes]
rs4985518	1.00[CEU][hapmap];0.93[GIH][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs4985523	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs55701476	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs55751101	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55863174	0.81[EUR][1000 genomes]
rs55992518	0.80[EUR][1000 genomes]
rs56316408	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57488237	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57565297	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60010276	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60099379	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs60472033	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61310815	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61426398	0.85[EUR][1000 genomes]
rs61460899	0.96[ASN][1000 genomes]
rs6499239	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6499253	0.82[EUR][1000 genomes]
rs6499255	1.00[CEU][hapmap];0.86[GIH][hapmap];0.83[TSI][hapmap]
rs689455	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs689460	0.81[YRI][hapmap]
rs7186002	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7187653	1.00[CEU][hapmap]
rs7189424	0.85[EUR][1000 genomes]
rs7190652	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7194753	1.00[CEU][hapmap];0.82[CHD][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap]
rs7196943	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7198242	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];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7200935	1.00[CEU][hapmap];0.84[CHD][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap]
rs72783115	0.99[ASN][1000 genomes]
rs73579458	0.82[EUR][1000 genomes]
rs74026882	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs74029403	0.84[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs8045142	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8045682	1.00[CEU][hapmap];0.95[GIH][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs8045705	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8046314	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8047885	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8052086	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8053080	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8054000	0.94[ASN][1000 genomes]
rs8054096	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8059345	0.82[EUR][1000 genomes]
rs8060588	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs920191	0.95[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9788803	0.98[ASN][1000 genomes]
rs9788837	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9921045	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9929720	1.00[CEU][hapmap];0.84[CHD][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap]
rs9933526	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9940548	0.88[ASN][1000 genomes]

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs10454066	SLC7A6	cis	cerebellum	SCAN
rs10454066	TPPP3	cis	parietal	SCAN
rs10454066	HPR	cis	cerebellum	SCAN
rs10454066	LOC440348	Cis_chr	lymphoblastoid	RTeQTL
rs10454066	HPR	cis	parietal	SCAN
rs10454066	LOC440348	cis	multi-tissue	Pritchard
rs10454066	NRN1L	cis	cerebellum	SCAN
rs10454066	FAM96B	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:69647600-69705000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr16:69654200-69703600	Weak transcription	Brain Angular Gyrus	brain
3	chr16:69654200-69705600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr16:69654600-69705000	Weak transcription	Psoas Muscle	Psoas
5	chr16:69660400-69709600	Weak transcription	Fetal Brain Male	brain
6	chr16:69667000-69727600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr16:69670800-69715400	Weak transcription	Aorta	Aorta
8	chr16:69671200-69726400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr16:69678800-69705600	Weak transcription	Stomach Mucosa	stomach
10	chr16:69680400-69699200	Strong transcription	Primary T helper cells PMA-I stimulated	--
11	chr16:69680600-69699200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr16:69680800-69699200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr16:69680800-69699200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr16:69680800-69699200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr16:69680800-69699200	Strong transcription	Liver	Liver
16	chr16:69681000-69699200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr16:69681400-69705200	Weak transcription	Small Intestine	intestine
18	chr16:69681600-69703000	Weak transcription	Brain Cingulate Gyrus	brain
19	chr16:69681600-69705400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr16:69681600-69709000	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr16:69681600-69711200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr16:69681600-69725800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr16:69681600-69725800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr16:69684600-69699200	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr16:69684800-69699200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr16:69685000-69699200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr16:69685000-69724800	Weak transcription	Fetal Heart	heart
28	chr16:69686800-69699200	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr16:69686800-69699200	Strong transcription	Primary T helper cells fromperipheralblood	blood
30	chr16:69687200-69699200	Strong transcription	Fetal Muscle Leg	muscle
31	chr16:69688400-69700000	Weak transcription	Right Atrium	heart
32	chr16:69688600-69704600	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr16:69688600-69725400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr16:69688800-69703400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr16:69689800-69705200	Weak transcription	Brain Germinal Matrix	brain
36	chr16:69690000-69705600	Weak transcription	Fetal Brain Female	brain
37	chr16:69690200-69703000	Weak transcription	Pancreas	Pancrea
38	chr16:69690200-69705400	Weak transcription	Gastric	stomach
39	chr16:69690200-69725800	Weak transcription	Ovary	ovary
40	chr16:69690400-69705600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr16:69690600-69705400	Weak transcription	Spleen	Spleen
42	chr16:69690800-69703200	Weak transcription	Brain Anterior Caudate	brain
43	chr16:69690800-69704600	Weak transcription	Right Ventricle	heart
44	chr16:69690800-69712400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr16:69691000-69726400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
46	chr16:69691200-69703000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr16:69691200-69706600	Weak transcription	Colon Smooth Muscle	Colon
48	chr16:69691400-69712400	Weak transcription	Colonic Mucosa	Colon
49	chr16:69692200-69699200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr16:69693000-69699200	Strong transcription	Osteobl	bone

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