Variant report

Variant	rs2286098
Chromosome Location	chr7:38786589-38786590
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 98 )
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];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10486678	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11971020	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11979618	0.90[ASN][1000 genomes]
rs11979824	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[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];0.90[ASN][1000 genomes]
rs12672885	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.96[AMR][1000 genomes];0.99[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];0.83[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];0.87[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17700392	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17700752	0.85[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap];0.91[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];0.87[YRI][hapmap];0.90[ASN][1000 genomes]
rs17768153	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17768212	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[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];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2074657	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.92[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];0.86[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2214666	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[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];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2240354	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2286082	0.97[ASN][1000 genomes]
rs2286084	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2286086	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs2286087	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2286088	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]
rs2286091	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2286094	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2286104	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.99[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];1.00[AMR][1000 genomes];0.99[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];0.96[AMR][1000 genomes];0.99[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	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60590111	0.90[ASN][1000 genomes]
rs62444078	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62444107	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[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	0.87[AMR][1000 genomes];0.96[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];0.98[AMR][1000 genomes];0.99[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]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2286098	VPS41	cis	lung	GTEx

Chromatin state (count:124 , 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	chr7:38755000-38791200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr7:38757200-38835400	Weak transcription	Psoas Muscle	Psoas
4	chr7:38759200-38810200	Weak transcription	A549	lung
5	chr7:38759400-38810600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr7:38760000-38799800	Weak transcription	HUVEC	blood vessel
7	chr7:38760600-38800200	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr7:38761000-38820400	Weak transcription	Stomach Mucosa	stomach
9	chr7:38762600-38793200	Weak transcription	Hela-S3	cervix
10	chr7:38763200-38828000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr7:38763400-38792600	Weak transcription	Small Intestine	intestine
12	chr7:38763400-38828800	Weak transcription	HepG2	liver
13	chr7:38763800-38791600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr7:38764400-38787600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr7:38765400-38789600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr7:38765400-38802800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr7:38766000-38791800	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr7:38766600-38791600	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr7:38767200-38792600	Weak transcription	Colonic Mucosa	Colon
20	chr7:38767200-38802800	Weak transcription	Right Ventricle	heart
21	chr7:38767200-38805800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr7:38768400-38791200	Weak transcription	Brain Germinal Matrix	brain
23	chr7:38768400-38791800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr7:38769800-38795000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr7:38774800-38787000	Strong transcription	Liver	Liver
26	chr7:38774800-38816800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr7:38775000-38787400	Strong transcription	Primary B cells from peripheral blood	blood
28	chr7:38775000-38788400	Strong transcription	Primary T cells from cord blood	blood
29	chr7:38775200-38787000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
30	chr7:38775600-38791200	Weak transcription	HSMMtube	muscle
31	chr7:38775800-38786800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr7:38775800-38787000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr7:38775800-38816600	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr7:38776000-38787600	Strong transcription	Primary T helper cells fromperipheralblood	blood
35	chr7:38776400-38792200	Weak transcription	Fetal Heart	heart
36	chr7:38777000-38786800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr7:38777200-38786600	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chr7:38777400-38800400	Strong transcription	Primary B cells from cord blood	blood
39	chr7:38779000-38788200	Strong transcription	Primary neutrophils fromperipheralblood	blood
40	chr7:38779200-38792800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr7:38779400-38786600	Strong transcription	Adipose Nuclei	Adipose
42	chr7:38779600-38786800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr7:38779600-38787400	Strong transcription	Fetal Intestine Large	intestine
44	chr7:38779600-38787600	Strong transcription	Dnd41	blood
45	chr7:38779800-38786600	Strong transcription	Primary T helper cells PMA-I stimulated	--
46	chr7:38779800-38786800	Strong transcription	Placenta	Placenta
47	chr7:38779800-38787400	Strong transcription	Primary T cells fromperipheralblood	blood
48	chr7:38779800-38787600	Strong transcription	Duodenum Mucosa	Duodenum
49	chr7:38779800-38794800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr7:38780000-38786600	Strong transcription	Primary hematopoietic stem cells	blood

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