Variant report

Variant	rs411862
Chromosome Location	chr13:48964825-48964826
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 79 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10076	1.00[CHD][hapmap];1.00[MEX][hapmap]
rs11840676	0.92[EUR][1000 genomes]
rs17071695	1.00[CHD][hapmap]
rs171989	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs174858	1.00[CHD][hapmap];1.00[GIH][hapmap]
rs185587	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs198559	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs198565	1.00[EUR][1000 genomes]
rs198566	1.00[EUR][1000 genomes]
rs198567	1.00[EUR][1000 genomes]
rs198572	1.00[EUR][1000 genomes]
rs198573	1.00[EUR][1000 genomes]
rs198583	1.00[EUR][1000 genomes]
rs198587	1.00[EUR][1000 genomes]
rs198600	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs198601	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs198613	1.00[EUR][1000 genomes]
rs198616	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs198617	1.00[ASW][hapmap];1.00[CHD][hapmap];0.91[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs198618	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs198626	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs198628	0.88[GIH][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs198632	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs198636	0.88[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2245534	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2265777	0.92[EUR][1000 genomes]
rs2406932	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2515668	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2804082	0.82[ASW][hapmap];0.82[MKK][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2804084	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2804085	0.83[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2804086	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2804087	1.00[EUR][1000 genomes]
rs2804088	1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs2804089	1.00[EUR][1000 genomes]
rs2804091	0.91[ASW][hapmap];0.82[LWK][hapmap];0.82[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2804092	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2854352	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2854354	0.82[YRI][hapmap]
rs2854356	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2854361	0.91[ASW][hapmap];1.00[CHD][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap]
rs2854363	1.00[EUR][1000 genomes]
rs2854364	1.00[EUR][1000 genomes]
rs2854365	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2984828	1.00[EUR][1000 genomes]
rs3020646	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs411661	0.92[EUR][1000 genomes]
rs4151590	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.92[EUR][1000 genomes]
rs416156	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs428431	1.00[EUR][1000 genomes]
rs449268	1.00[CHD][hapmap];1.00[GIH][hapmap]
rs4587857	0.84[EUR][1000 genomes]
rs4625624	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs547747	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61507973	0.92[EUR][1000 genomes]
rs7318012	1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs7332631	1.00[CHD][hapmap];1.00[MEX][hapmap]
rs7990103	1.00[EUR][1000 genomes]
rs8001351	0.92[EUR][1000 genomes]
rs9285166	0.92[EUR][1000 genomes]
rs9316371	0.92[EUR][1000 genomes]
rs9316386	1.00[CHD][hapmap]
rs9316392	1.00[CHD][hapmap];1.00[MEX][hapmap]
rs9316396	1.00[CHD][hapmap]
rs9332025	1.00[CHD][hapmap];1.00[MEX][hapmap]
rs9332053	0.93[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9332066	1.00[CHD][hapmap];1.00[MEX][hapmap];0.82[EUR][1000 genomes]
rs9332248	0.92[EUR][1000 genomes]
rs9332281	1.00[CHD][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs9562817	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9591153	0.92[EUR][1000 genomes]
rs9591154	0.92[EUR][1000 genomes]
rs9591155	0.92[EUR][1000 genomes]
rs9591163	1.00[EUR][1000 genomes]
rs9591171	1.00[CHD][hapmap];1.00[MEX][hapmap]
rs9595872	0.91[EUR][1000 genomes]
rs9595894	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9595909	1.00[EUR][1000 genomes]
rs9595910	1.00[EUR][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs411862	RCBTB2	cis	lymphoblastoid	seeQTL

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:48909000-48972200	Weak transcription	NHEK	skin
2	chr13:48912200-48968200	Weak transcription	Brain Cingulate Gyrus	brain
3	chr13:48914000-48965800	Weak transcription	Lung	lung
4	chr13:48914800-48972000	Weak transcription	NHLF	lung
5	chr13:48916800-48985400	Weak transcription	Colonic Mucosa	Colon
6	chr13:48918600-48967200	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr13:48920200-48974400	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr13:48921600-48972000	Weak transcription	Stomach Mucosa	stomach
9	chr13:48925200-48974800	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr13:48925400-48976400	Weak transcription	Ovary	ovary
11	chr13:48925600-48968000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr13:48926800-48972000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr13:48928200-48971800	Weak transcription	A549	lung
14	chr13:48929800-48968400	Weak transcription	Esophagus	oesophagus
15	chr13:48933400-48974000	Weak transcription	Rectal Smooth Muscle	rectum
16	chr13:48934600-48984200	Weak transcription	Right Ventricle	heart
17	chr13:48935400-48968200	Weak transcription	Spleen	Spleen
18	chr13:48936000-48974600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr13:48936200-48968200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr13:48936400-48973200	Weak transcription	Hela-S3	cervix
21	chr13:48941800-48973200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr13:48942400-48967200	Weak transcription	Brain Germinal Matrix	brain
23	chr13:48943000-48970800	Weak transcription	Pancreas	Pancrea
24	chr13:48943600-48984200	Weak transcription	Brain Angular Gyrus	brain
25	chr13:48944000-48974400	Weak transcription	Brain Anterior Caudate	brain
26	chr13:48944200-48973800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr13:48944600-48965600	Weak transcription	Aorta	Aorta
28	chr13:48944600-48983400	Weak transcription	Psoas Muscle	Psoas
29	chr13:48945000-48966000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr13:48945000-48972000	Weak transcription	HSMMtube	muscle
31	chr13:48945200-48967000	Weak transcription	HepG2	liver
32	chr13:48945400-48974400	Weak transcription	Small Intestine	intestine
33	chr13:48949200-48967800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr13:48949400-48972800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr13:48949600-48965400	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr13:48949600-48968200	Weak transcription	Duodenum Mucosa	Duodenum
37	chr13:48949600-48968200	Weak transcription	Fetal Kidney	kidney
38	chr13:48950000-48967800	Weak transcription	Stomach Smooth Muscle	stomach
39	chr13:48950000-48967800	Weak transcription	Thymus	Thymus
40	chr13:48950000-48968200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr13:48950600-48965600	Weak transcription	Left Ventricle	heart
42	chr13:48950600-48968400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr13:48951200-48965400	Weak transcription	Placenta	Placenta
44	chr13:48952600-48967400	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr13:48953800-48965400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr13:48953800-48972000	Weak transcription	Osteobl	bone
47	chr13:48954000-48965600	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr13:48954400-48972200	Weak transcription	HUVEC	blood vessel
49	chr13:48954800-48967200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr13:48954800-48967200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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