Variant report

Variant	rs2286088
Chromosome Location	chr7:38799722-38799723
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:38795817..38798260-chr7:38798737..38800298,2	K562	blood:
2	chr7:38795817..38798538-chr7:38798737..38800643,4	K562	blood:
3	chr7:38798102..38800660-chr7:38801765..38803412,2	K562	blood:

Extended variants
information (count: 97 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs1017028	0.95[ASN][1000 genomes]
rs10242048	0.94[ASN][1000 genomes]
rs10247503	0.95[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs10251912	0.99[ASN][1000 genomes]
rs10254567	0.99[ASN][1000 genomes]
rs10271176	0.99[ASN][1000 genomes]
rs10486677	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10486678	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11971020	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11979618	0.90[ASN][1000 genomes]
rs11979824	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11980882	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs12533557	0.99[ASN][1000 genomes]
rs12672237	0.90[ASN][1000 genomes]
rs12672750	0.90[ASN][1000 genomes]
rs12672793	0.87[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.90[ASN][1000 genomes]
rs12672885	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12674115	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs12701652	0.80[JPT][hapmap]
rs12701659	0.88[ASN][1000 genomes]
rs1468348	0.86[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs17700072	0.85[ASN][1000 genomes]
rs17700142	0.91[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.90[ASN][1000 genomes]
rs17700172	0.86[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs17700190	0.90[ASN][1000 genomes]
rs17700262	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17700392	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17700752	0.85[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap];0.95[YRI][hapmap];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17767695	0.88[ASN][1000 genomes]
rs17767770	0.88[ASN][1000 genomes]
rs17767818	0.91[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.90[ASN][1000 genomes]
rs17768153	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17768212	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17768711	0.94[CHB][hapmap]
rs17768753	0.86[JPT][hapmap]
rs1859494	0.88[ASN][1000 genomes]
rs1859937	0.84[CHB][hapmap];0.81[JPT][hapmap]
rs1978171	0.86[ASN][1000 genomes]
rs1978172	0.86[ASN][1000 genomes]
rs2074655	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2074657	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2107743	0.99[ASN][1000 genomes]
rs2108507	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs2189855	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2214666	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2240351	0.96[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs2240352	0.95[CHB][hapmap];0.90[JPT][hapmap];0.98[ASN][1000 genomes]
rs2240353	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2240354	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2286082	0.97[ASN][1000 genomes]
rs2286084	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2286086	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs2286087	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2286091	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2286094	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2286098	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2286104	1.00[CEU][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2286105	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2286106	0.95[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs2286109	0.91[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs2392598	0.86[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs28548028	0.99[ASN][1000 genomes]
rs34724372	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs35253728	0.88[ASN][1000 genomes]
rs35791079	0.88[ASN][1000 genomes]
rs3735347	0.86[CHB][hapmap];0.88[ASN][1000 genomes]
rs3801139	0.95[CHB][hapmap];0.90[JPT][hapmap];0.98[ASN][1000 genomes]
rs3801140	0.95[CHB][hapmap];0.90[JPT][hapmap];0.98[ASN][1000 genomes]
rs3801141	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3801143	0.95[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs3801145	0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs3801146	0.99[ASN][1000 genomes]
rs4723782	0.99[ASN][1000 genomes]
rs4723785	0.96[CHB][hapmap];0.91[JPT][hapmap];0.99[ASN][1000 genomes]
rs56002981	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56050717	0.87[ASN][1000 genomes]
rs57091471	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60590111	0.90[ASN][1000 genomes]
rs62444078	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62444107	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6462860	0.89[ASN][1000 genomes]
rs66662538	0.90[ASN][1000 genomes]
rs66796288	0.88[ASN][1000 genomes]
rs66976998	0.86[ASN][1000 genomes]
rs67202646	0.89[ASN][1000 genomes]
rs733150	0.96[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs73368205	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7778570	0.86[ASN][1000 genomes]
rs7779329	0.86[ASN][1000 genomes]
rs7780625	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs7783546	0.88[ASN][1000 genomes]
rs7785911	0.95[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs7786389	1.00[CEU][hapmap];0.90[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7794030	0.88[ASN][1000 genomes]
rs7795874	0.95[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs7797871	0.89[ASN][1000 genomes]
rs886646	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2286088	VPS41	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:38749000-38803600	Weak transcription	Fetal Brain Male	brain
2	chr7:38757200-38835400	Weak transcription	Psoas Muscle	Psoas
3	chr7:38759200-38810200	Weak transcription	A549	lung
4	chr7:38759400-38810600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr7:38760000-38799800	Weak transcription	HUVEC	blood vessel
6	chr7:38760600-38800200	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr7:38761000-38820400	Weak transcription	Stomach Mucosa	stomach
8	chr7:38763200-38828000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr7:38763400-38828800	Weak transcription	HepG2	liver
10	chr7:38765400-38802800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr7:38767200-38802800	Weak transcription	Right Ventricle	heart
12	chr7:38767200-38805800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr7:38774800-38816800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr7:38775800-38816600	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr7:38777400-38800400	Strong transcription	Primary B cells from cord blood	blood
16	chr7:38780800-38803600	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr7:38780800-38806000	Weak transcription	Fetal Brain Female	brain
18	chr7:38780800-38828800	Weak transcription	Gastric	stomach
19	chr7:38781400-38805800	Weak transcription	Brain Substantia Nigra	brain
20	chr7:38784400-38805800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr7:38784600-38805800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr7:38784800-38835000	Weak transcription	NHEK	skin
23	chr7:38785000-38815800	Weak transcription	NHLF	lung
24	chr7:38785600-38834600	Weak transcription	HMEC	breast
25	chr7:38785600-38835000	Weak transcription	NH-A	brain
26	chr7:38786600-38805800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr7:38786600-38805800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr7:38786600-38806000	Weak transcription	Brain Cingulate Gyrus	brain
29	chr7:38787000-38827400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr7:38789000-38800000	Strong transcription	Primary T helper cells fromperipheralblood	blood
31	chr7:38789000-38818800	Strong transcription	Primary B cells from peripheral blood	blood
32	chr7:38789200-38800000	Strong transcription	Fetal Intestine Large	intestine
33	chr7:38789600-38800000	Strong transcription	Liver	Liver
34	chr7:38789600-38800200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr7:38789600-38811000	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr7:38789600-38816800	Strong transcription	Primary T cells fromperipheralblood	blood
37	chr7:38790200-38800000	Strong transcription	Primary T helper cells PMA-I stimulated	--
38	chr7:38791200-38802600	Weak transcription	Brain Anterior Caudate	brain
39	chr7:38791400-38812600	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr7:38791600-38801600	Weak transcription	HSMM	muscle
41	chr7:38791800-38801600	Weak transcription	NHDF-Ad	bronchial
42	chr7:38791800-38813400	Weak transcription	Osteobl	bone
43	chr7:38791800-38814200	Weak transcription	K562	blood
44	chr7:38792000-38802200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr7:38792000-38802800	Weak transcription	Fetal Thymus	thymus
46	chr7:38792000-38810800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr7:38792000-38812600	Weak transcription	Brain Germinal Matrix	brain
48	chr7:38792200-38802400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr7:38792200-38803600	Weak transcription	Thymus	Thymus
50	chr7:38792200-38828000	Weak transcription	Colon Smooth Muscle	Colon

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