Variant report

Variant	rs2286093
Chromosome Location	chr7:38789213-38789214
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:38787918..38790102-chr7:38792675..38794796,2	MCF-7	breast:

Extended variants
information (count: 114 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:113)

rs_ID	r²[population]
rs10085487	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs1012976	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10224856	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10225415	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10225550	1.00[CHB][hapmap]
rs10229055	1.00[CHB][hapmap]
rs10242407	0.81[EUR][1000 genomes]
rs10254354	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10270427	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10275873	1.00[CHB][hapmap]
rs10951574	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10951575	1.00[JPT][hapmap]
rs12112381	1.00[YRI][hapmap]
rs12701653	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12701656	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12701657	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12701661	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12701671	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes]
rs13224619	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];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	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13231372	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs13235997	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13236092	0.81[EUR][1000 genomes]
rs13238093	0.80[EUR][1000 genomes]
rs1558111	1.00[CHB][hapmap]
rs17240051	1.00[ASN][1000 genomes]
rs17680342	1.00[CEU][hapmap]
rs2040878	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]
rs2058073	0.85[EUR][1000 genomes]
rs2107742	1.00[JPT][hapmap]
rs2108508	0.81[EUR][1000 genomes]
rs2189854	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2190667	1.00[CHB][hapmap]
rs2190668	0.81[EUR][1000 genomes]
rs2190670	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs2214667	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2214668	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2215032	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2245773	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2286089	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]
rs2286101	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]
rs2286103	1.00[JPT][hapmap]
rs2392599	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]
rs2392608	1.00[CHB][hapmap]
rs2392610	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs34349310	0.80[EUR][1000 genomes]
rs34358406	0.80[EUR][1000 genomes]
rs34621392	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34886315	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	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35632362	0.80[EUR][1000 genomes]
rs35667896	0.91[EUR][1000 genomes]
rs35816439	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35843038	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36004953	0.91[EUR][1000 genomes]
rs36114334	0.94[EUR][1000 genomes]
rs36121032	0.81[EUR][1000 genomes]
rs37472	1.00[JPT][hapmap]
rs37473	1.00[JPT][hapmap]
rs37476	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs37477	1.00[JPT][hapmap]
rs37478	1.00[JPT][hapmap]
rs37479	1.00[JPT][hapmap]
rs40445	0.81[EUR][1000 genomes]
rs4720300	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4720302	1.00[JPT][hapmap]
rs4723780	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4723781	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4723784	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]
rs4723786	1.00[JPT][hapmap]
rs4723787	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4723802	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4723804	1.00[ASN][1000 genomes]
rs57617719	0.94[AFR][1000 genomes]
rs58454657	0.91[AFR][1000 genomes]
rs6462866	1.00[JPT][hapmap]
rs6462871	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs6462873	1.00[CHB][hapmap]
rs6947695	1.00[CHB][hapmap]
rs6949958	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]
rs6951429	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6960945	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6963090	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6967384	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6971632	1.00[CHB][hapmap]
rs6975410	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6976302	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6976579	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6976580	1.00[CHB][hapmap]
rs6979423	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs71548633	0.83[EUR][1000 genomes]
rs73368230	0.81[AFR][1000 genomes]
rs73370730	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs757685	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs758087	1.00[JPT][hapmap]
rs758088	1.00[ASN][1000 genomes]
rs7782140	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7782277	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7787423	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]
rs7790054	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs7793250	1.00[CHB][hapmap]
rs7799887	1.00[CHB][hapmap]
rs7802052	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7802623	0.91[AFR][1000 genomes]
rs7803488	1.00[CHB][hapmap]
rs9638945	1.00[CHB][hapmap]
rs976350	1.00[JPT][hapmap]
rs976352	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9886108	1.00[CHB][hapmap]

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
rs2286093	VPS41	Cis_1M	lymphoblastoid	RTeQTL

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	chr7:38765400-38789600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr7:38765400-38802800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr7:38766000-38791800	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr7:38766600-38791600	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr7:38767200-38792600	Weak transcription	Colonic Mucosa	Colon
19	chr7:38767200-38802800	Weak transcription	Right Ventricle	heart
20	chr7:38767200-38805800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr7:38768400-38791200	Weak transcription	Brain Germinal Matrix	brain
22	chr7:38768400-38791800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr7:38769800-38795000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr7:38774800-38816800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr7:38775600-38791200	Weak transcription	HSMMtube	muscle
26	chr7:38775800-38816600	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr7:38776400-38792200	Weak transcription	Fetal Heart	heart
28	chr7:38777400-38800400	Strong transcription	Primary B cells from cord blood	blood
29	chr7:38779200-38792800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr7:38779800-38794800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr7:38780000-38792000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr7:38780800-38790200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr7:38780800-38792800	Weak transcription	Rectal Smooth Muscle	rectum
34	chr7:38780800-38803600	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr7:38780800-38806000	Weak transcription	Fetal Brain Female	brain
36	chr7:38780800-38828800	Weak transcription	Gastric	stomach
37	chr7:38781400-38790400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr7:38781400-38805800	Weak transcription	Brain Substantia Nigra	brain
39	chr7:38782000-38790200	Weak transcription	Brain Hippocampus Middle	brain
40	chr7:38782200-38791200	Weak transcription	K562	blood
41	chr7:38782600-38791400	Weak transcription	Brain Angular Gyrus	brain
42	chr7:38783000-38791400	Weak transcription	Colon Smooth Muscle	Colon
43	chr7:38783200-38789600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr7:38783200-38790800	Weak transcription	Brain Anterior Caudate	brain
45	chr7:38783200-38791400	Weak transcription	Ovary	ovary
46	chr7:38784000-38791400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr7:38784400-38791200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr7:38784400-38805800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr7:38784600-38789400	Weak transcription	Fetal Thymus	thymus
50	chr7:38784600-38789600	Weak transcription	Rectal Mucosa Donor 31	rectum

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