Variant report

Variant	rs7802052
Chromosome Location	chr7:38792800-38792801
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:38777448..38781271-chr7:38790893..38794034,3	K562	blood:
2	chr7:38787918..38790102-chr7:38792675..38794796,2	MCF-7	breast:
3	chr7:38787332..38789165-chr7:38790853..38793676,2	K562	blood:

Extended variants
information (count: 77 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10085487	0.81[EUR][1000 genomes]
rs1012976	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10224856	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10225415	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10242407	0.81[EUR][1000 genomes]
rs10254354	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10270427	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10951574	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12701656	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12701657	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12701661	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12701671	0.91[EUR][1000 genomes]
rs13224619	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13224857	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13229445	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13230196	0.92[EUR][1000 genomes]
rs13231372	0.81[EUR][1000 genomes]
rs13235997	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13236092	0.81[EUR][1000 genomes]
rs13238093	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs17240051	1.00[ASN][1000 genomes]
rs2040878	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2058073	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2108508	0.81[EUR][1000 genomes]
rs2189854	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2190668	0.81[EUR][1000 genomes]
rs2190670	0.81[EUR][1000 genomes]
rs2214667	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2214668	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2215032	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2245773	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2286089	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2286093	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2286101	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2392599	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2392610	1.00[ASN][1000 genomes]
rs34349310	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs34358406	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs34621392	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34886315	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34997080	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35220172	1.00[ASN][1000 genomes]
rs35400125	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35632362	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs35667896	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35816439	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35843038	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36004953	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs36114334	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs36121032	0.81[EUR][1000 genomes]
rs37476	0.81[EUR][1000 genomes]
rs40445	0.81[EUR][1000 genomes]
rs4720300	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4723780	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4723781	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4723784	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4723787	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4723804	1.00[ASN][1000 genomes]
rs6949958	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6951429	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6960945	1.00[ASN][1000 genomes]
rs6963090	1.00[ASN][1000 genomes]
rs6967384	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6975410	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6976302	1.00[ASN][1000 genomes]
rs6976579	1.00[ASN][1000 genomes]
rs6979423	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs71548633	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73370730	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs757685	1.00[ASN][1000 genomes]
rs758088	1.00[ASN][1000 genomes]
rs7782140	1.00[ASN][1000 genomes]
rs7782277	1.00[ASN][1000 genomes]
rs7787423	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7790054	0.81[EUR][1000 genomes]
rs976352	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	nsv887965	chr7:38706384-38793243	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7802052	VPS41	Cis_1M	lymphoblastoid	RTeQTL
rs7802052	FAM183B	cis	lung	GTEx

Chromatin state (count:134 , 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	chr7:38762600-38793200	Weak transcription	Hela-S3	cervix
9	chr7:38763200-38828000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr7:38763400-38828800	Weak transcription	HepG2	liver
11	chr7:38765400-38802800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr7:38767200-38802800	Weak transcription	Right Ventricle	heart
13	chr7:38767200-38805800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr7:38769800-38795000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr7:38774800-38816800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr7:38775800-38816600	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr7:38777400-38800400	Strong transcription	Primary B cells from cord blood	blood
18	chr7:38779200-38792800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr7:38779800-38794800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr7:38780800-38792800	Weak transcription	Rectal Smooth Muscle	rectum
21	chr7:38780800-38803600	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr7:38780800-38806000	Weak transcription	Fetal Brain Female	brain
23	chr7:38780800-38828800	Weak transcription	Gastric	stomach
24	chr7:38781400-38805800	Weak transcription	Brain Substantia Nigra	brain
25	chr7:38784400-38805800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr7:38784600-38805800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr7:38784800-38835000	Weak transcription	NHEK	skin
28	chr7:38785000-38815800	Weak transcription	NHLF	lung
29	chr7:38785600-38834600	Weak transcription	HMEC	breast
30	chr7:38785600-38835000	Weak transcription	NH-A	brain
31	chr7:38786600-38792800	Weak transcription	Pancreas	Pancrea
32	chr7:38786600-38792800	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr7:38786600-38794800	Weak transcription	Fetal Intestine Small	intestine
34	chr7:38786600-38805800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr7:38786600-38805800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr7:38786600-38806000	Weak transcription	Brain Cingulate Gyrus	brain
37	chr7:38787000-38827400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr7:38787200-38797000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr7:38789000-38797400	Strong transcription	Primary neutrophils fromperipheralblood	blood
40	chr7:38789000-38800000	Strong transcription	Primary T helper cells fromperipheralblood	blood
41	chr7:38789000-38818800	Strong transcription	Primary B cells from peripheral blood	blood
42	chr7:38789200-38800000	Strong transcription	Fetal Intestine Large	intestine
43	chr7:38789400-38795000	Strong transcription	Fetal Muscle Trunk	muscle
44	chr7:38789400-38795600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr7:38789400-38795800	Strong transcription	Primary T cells from cord blood	blood
46	chr7:38789400-38799600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr7:38789600-38793800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr7:38789600-38794400	Strong transcription	Duodenum Mucosa	Duodenum
49	chr7:38789600-38794800	Strong transcription	Duodenum Smooth Muscle	Duodenum
50	chr7:38789600-38795000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland

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