Variant report

Variant	rs713243
Chromosome Location	chr7:38871105-38871106
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1001476	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs10085898	0.83[YRI][hapmap]
rs10486680	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs10951573	0.90[CEU][hapmap]
rs11970960	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs11971030	0.96[EUR][1000 genomes]
rs11977016	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11978816	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11980534	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs11982889	1.00[CEU][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs11984145	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12112141	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs13231320	0.90[CEU][hapmap]
rs1557941	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs16879964	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs16879966	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs17171465	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs17171466	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs28680843	1.00[EUR][1000 genomes]
rs34753378	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs60354841	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs68175808	0.96[EUR][1000 genomes]
rs6962120	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6976100	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs73113674	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73113680	0.96[EUR][1000 genomes]
rs73113689	0.96[EUR][1000 genomes]
rs73113699	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73115614	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73115622	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73115623	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73115628	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73121378	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73121380	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73121381	0.96[EUR][1000 genomes]
rs73121384	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73121386	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73121396	1.00[EUR][1000 genomes]
rs73121399	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73123603	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73123614	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73123618	1.00[EUR][1000 genomes]
rs73123621	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73123624	1.00[EUR][1000 genomes]
rs73123626	1.00[EUR][1000 genomes]
rs73123893	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73125633	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7812184	1.00[CEU][hapmap];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032637	chr7:38832627-38902723	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv887966	chr7:38835035-38933942	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs713243	VPS41	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:38831000-38871200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr7:38835600-38900800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr7:38856200-38871200	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr7:38857600-38871800	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr7:38858400-38871800	Weak transcription	Lung	lung
6	chr7:38858600-38901600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr7:38858800-38907600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr7:38859000-38872800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr7:38859000-38895200	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr7:38859800-38900800	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr7:38860600-38900200	Weak transcription	Fetal Intestine Large	intestine
12	chr7:38863000-38876800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr7:38863000-38888200	Weak transcription	Fetal Intestine Small	intestine
14	chr7:38863800-38879600	Weak transcription	Fetal Lung	lung
15	chr7:38864000-38874000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr7:38864200-38871200	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr7:38865600-38873000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr7:38865800-38871200	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr7:38865800-38872800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr7:38865800-38879600	Weak transcription	Right Atrium	heart
21	chr7:38866000-38872400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr7:38866000-38886400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr7:38866400-38876800	Weak transcription	Primary hematopoietic stem cells	blood
24	chr7:38866400-38877000	Weak transcription	Primary T cells from cord blood	blood
25	chr7:38866800-38877000	Weak transcription	Primary B cells from cord blood	blood
26	chr7:38867200-38876800	Weak transcription	Primary B cells from peripheral blood	blood
27	chr7:38867400-38871800	Weak transcription	Fetal Brain Female	brain
28	chr7:38867400-38872800	Weak transcription	Ovary	ovary
29	chr7:38867400-38872800	Weak transcription	Pancreas	Pancrea
30	chr7:38867400-38873000	Weak transcription	Gastric	stomach
31	chr7:38867400-38877800	Weak transcription	Fetal Brain Male	brain
32	chr7:38867400-38905200	Weak transcription	Left Ventricle	heart
33	chr7:38867600-38879600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr7:38868800-38873800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr7:38869600-38871200	Enhancers	Stomach Mucosa	stomach
36	chr7:38869600-38888400	Weak transcription	Primary monocytes fromperipheralblood	blood
37	chr7:38869800-38871400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
38	chr7:38870000-38871400	Enhancers	Brain Hippocampus Middle	brain
39	chr7:38870000-38876600	Weak transcription	GM12878-XiMat	blood
40	chr7:38870000-38888200	Weak transcription	Monocytes-CD14+_RO01746	blood
41	chr7:38870000-38895600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr7:38870200-38895600	Weak transcription	Primary T helper cells fromperipheralblood	blood
43	chr7:38870400-38871600	Enhancers	ES-I3 Cell Line	embryonic stem cell
44	chr7:38870600-38871200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr7:38870600-38871200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr7:38870600-38871600	Enhancers	iPS-18 Cell Line	embryonic stem cell
47	chr7:38870600-38871600	Enhancers	iPS-20b Cell Line	embryonic stem cell
48	chr7:38870600-38871600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr7:38870600-38871600	Active TSS	Colon Smooth Muscle	Colon
50	chr7:38870600-38871600	Active TSS	Pancreatic Islets	Pancreatic Islet

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