Variant report

Variant	rs2189855
Chromosome Location	chr7:38771312-38771313
allele	A/C
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[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10486678	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11971020	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11979618	0.81[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs11979824	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11980882	0.89[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	0.90[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.90[ASN][1000 genomes]
rs12672885	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12674115	0.84[CHB][hapmap];0.86[JPT][hapmap]
rs12701652	0.80[JPT][hapmap]
rs12701659	0.88[ASN][1000 genomes]
rs1468348	0.89[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs17700072	0.85[ASN][1000 genomes]
rs17700142	0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs17700172	0.89[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs17700190	0.90[ASN][1000 genomes]
rs17700262	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17700392	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17700752	0.90[CHB][hapmap];0.89[JPT][hapmap];0.85[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	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs17768153	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17768212	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17768711	0.93[CHB][hapmap]
rs17768753	0.86[JPT][hapmap]
rs1859494	0.88[ASN][1000 genomes]
rs1859937	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs1978171	0.86[ASN][1000 genomes]
rs1978172	0.86[ASN][1000 genomes]
rs2074655	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2074657	1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2107743	0.99[ASN][1000 genomes]
rs2108507	0.84[CHB][hapmap];0.90[JPT][hapmap]
rs2214666	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2240351	0.95[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs2240352	0.94[CHB][hapmap];0.90[JPT][hapmap];0.98[ASN][1000 genomes]
rs2240353	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2240354	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2286082	0.97[ASN][1000 genomes]
rs2286084	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2286086	0.94[CHB][hapmap];0.95[JPT][hapmap]
rs2286087	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2286088	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]
rs2286091	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2286094	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2286098	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]
rs2286104	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2286105	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2286106	0.94[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs2286109	0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs2392598	0.83[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs28548028	0.99[ASN][1000 genomes]
rs34724372	0.89[CHB][hapmap];0.86[JPT][hapmap]
rs35253728	0.88[ASN][1000 genomes]
rs35791079	0.88[ASN][1000 genomes]
rs3735347	0.89[CHB][hapmap];0.88[ASN][1000 genomes]
rs3801139	0.94[CHB][hapmap];0.90[JPT][hapmap];0.98[ASN][1000 genomes]
rs3801140	0.94[CHB][hapmap];0.90[JPT][hapmap];0.98[ASN][1000 genomes]
rs3801141	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3801143	0.94[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs3801145	0.94[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs3801146	0.99[ASN][1000 genomes]
rs4723782	0.99[ASN][1000 genomes]
rs4723785	0.95[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	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60590111	0.90[ASN][1000 genomes]
rs62444078	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62444107	0.94[AFR][1000 genomes];0.96[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	0.95[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs73368205	0.87[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	0.84[CHB][hapmap];0.90[JPT][hapmap]
rs7783546	0.88[ASN][1000 genomes]
rs7785911	0.94[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs7786389	0.84[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7794030	0.88[ASN][1000 genomes]
rs7795874	0.94[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs7797871	0.89[ASN][1000 genomes]
rs886646	0.94[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
rs2189855	VPS41	cis	lung	GTEx

Chromatin state (count:120 , 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	chr7:38755800-38771600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr7:38757000-38784200	Weak transcription	HMEC	breast
5	chr7:38757200-38835400	Weak transcription	Psoas Muscle	Psoas
6	chr7:38758600-38780600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr7:38758800-38780000	Weak transcription	Brain Substantia Nigra	brain
8	chr7:38759200-38810200	Weak transcription	A549	lung
9	chr7:38759400-38810600	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr7:38759600-38779600	Weak transcription	Thymus	Thymus
11	chr7:38759600-38784200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr7:38759800-38780600	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr7:38760000-38773000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr7:38760000-38799800	Weak transcription	HUVEC	blood vessel
15	chr7:38760600-38800200	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr7:38761000-38820400	Weak transcription	Stomach Mucosa	stomach
17	chr7:38761200-38785400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr7:38762600-38793200	Weak transcription	Hela-S3	cervix
19	chr7:38763200-38828000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr7:38763400-38780400	Weak transcription	Fetal Kidney	kidney
21	chr7:38763400-38792600	Weak transcription	Small Intestine	intestine
22	chr7:38763400-38828800	Weak transcription	HepG2	liver
23	chr7:38763600-38772000	Strong transcription	Liver	Liver
24	chr7:38763800-38791600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr7:38764200-38772000	Strong transcription	Rectal Mucosa Donor 29	rectum
26	chr7:38764200-38772800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr7:38764400-38771800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr7:38764400-38787600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr7:38764800-38775000	Weak transcription	Fetal Heart	heart
30	chr7:38764800-38775200	Weak transcription	HSMMtube	muscle
31	chr7:38764800-38784200	Weak transcription	NHEK	skin
32	chr7:38765400-38784200	Weak transcription	NHLF	lung
33	chr7:38765400-38789600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr7:38765400-38802800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr7:38765600-38779600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr7:38765600-38779600	Weak transcription	Spleen	Spleen
37	chr7:38765600-38784200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr7:38765600-38784400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr7:38766000-38784200	Weak transcription	NH-A	brain
40	chr7:38766000-38791800	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr7:38766200-38780000	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr7:38766200-38783400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr7:38766600-38780600	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr7:38766600-38782600	Weak transcription	Colon Smooth Muscle	Colon
45	chr7:38766600-38791600	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr7:38766800-38772800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr7:38766800-38784200	Weak transcription	NHDF-Ad	bronchial
48	chr7:38767000-38779200	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr7:38767200-38779800	Weak transcription	Primary T helper cells PMA-I stimulated	--
50	chr7:38767200-38779800	Weak transcription	Rectal Smooth Muscle	rectum

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