Variant report

Variant	rs3798853
Chromosome Location	chr6:127636823-127636824
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 102 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs1073931	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1073932	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10872312	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11961994	0.84[TSI][hapmap]
rs12199451	0.84[TSI][hapmap]
rs13218061	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1543432	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1964130	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2038378	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2057223	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2144742	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2144743	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2180341	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2281491	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2326567	1.00[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];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2875972	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3756996	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3798850	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3798852	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3798857	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3798859	0.84[TSI][hapmap]
rs4280986	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4448121	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4472373	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4486042	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4895821	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4895822	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4895823	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4897207	0.93[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6569477	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6569478	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6569479	0.93[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];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6569480	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6569482	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6569483	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6569486	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs67371475	0.86[EUR][1000 genomes]
rs6900074	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6903878	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6904520	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6904630	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6904834	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6906717	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6909703	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6910763	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6913350	0.86[EUR][1000 genomes]
rs6913424	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6916990	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6930849	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6937287	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7449576	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7453272	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap]
rs7739679	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7742161	0.86[EUR][1000 genomes]
rs7745944	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7751865	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7752238	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7753913	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7756336	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7756880	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7756884	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7760652	0.86[EUR][1000 genomes]
rs7760748	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7766942	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7771923	0.91[EUR][1000 genomes]
rs7773484	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7774468	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7775493	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7776136	0.93[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];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs877102	0.81[CEU][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs877661	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs910720	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9285459	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9285460	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9321073	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9321074	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9321076	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9321079	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9372860	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9375492	0.85[CEU][hapmap];0.89[CHB][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.85[MEX][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9375495	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9375499	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9375501	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9375503	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9385419	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9388553	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9388554	0.86[EUR][1000 genomes]
rs9388555	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9388561	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9388568	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9388571	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9398836	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9398837	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9398838	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9398839	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9398840	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9398841	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9398842	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9401950	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9401951	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9401952	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9401953	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.82[YRI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3798853	TRMT11	cis	parietal	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:127605000-127660800	Weak transcription	Hela-S3	cervix
2	chr6:127608800-127646800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr6:127608800-127646800	Weak transcription	Lung	lung
4	chr6:127608800-127652800	Weak transcription	Esophagus	oesophagus
5	chr6:127608800-127653600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr6:127608800-127653600	Weak transcription	Pancreas	Pancrea
7	chr6:127608800-127654600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr6:127608800-127661400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr6:127608800-127663600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr6:127608800-127663600	Weak transcription	Gastric	stomach
11	chr6:127609000-127646200	Weak transcription	Psoas Muscle	Psoas
12	chr6:127611400-127645600	Weak transcription	Duodenum Mucosa	Duodenum
13	chr6:127612200-127637600	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr6:127613000-127640000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr6:127613000-127661000	Weak transcription	Small Intestine	intestine
16	chr6:127613400-127646200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr6:127614600-127659200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr6:127616600-127645800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr6:127618800-127647200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr6:127620400-127647000	Weak transcription	Left Ventricle	heart
21	chr6:127621800-127646400	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr6:127621800-127661000	Weak transcription	Fetal Heart	heart
23	chr6:127622000-127645200	Weak transcription	HMEC	breast
24	chr6:127622000-127645600	Weak transcription	HSMMtube	muscle
25	chr6:127622000-127646800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr6:127622000-127646800	Weak transcription	Aorta	Aorta
27	chr6:127622000-127649400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr6:127622000-127661400	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr6:127622000-127661400	Weak transcription	NHEK	skin
30	chr6:127622800-127661400	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr6:127622800-127662600	Weak transcription	Fetal Brain Male	brain
32	chr6:127623000-127649200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr6:127624000-127646400	Weak transcription	HUVEC	blood vessel
34	chr6:127625600-127646000	Weak transcription	Thymus	Thymus
35	chr6:127625600-127661400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr6:127626000-127646000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr6:127627400-127639200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr6:127627400-127659000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr6:127627800-127645800	Weak transcription	Brain Germinal Matrix	brain
40	chr6:127627800-127646800	Weak transcription	Fetal Intestine Small	intestine
41	chr6:127628000-127653000	Weak transcription	Brain Hippocampus Middle	brain
42	chr6:127629400-127644800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr6:127629800-127661200	Weak transcription	A549	lung
44	chr6:127630000-127637600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr6:127630000-127638800	Weak transcription	Stomach Smooth Muscle	stomach
46	chr6:127630200-127637400	Strong transcription	Monocytes-CD14+_RO01746	blood
47	chr6:127630200-127642600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr6:127630400-127637200	Strong transcription	Liver	Liver
49	chr6:127630400-127646000	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr6:127630400-127647200	Weak transcription	Brain Inferior Temporal Lobe	brain

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