Variant report

Variant	rs28680843
Chromosome Location	chr7:38869571-38869572
allele	C/T
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	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10249090	0.81[AFR][1000 genomes]
rs10486680	0.94[EUR][1000 genomes]
rs11970960	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11971030	0.96[EUR][1000 genomes]
rs11977016	1.00[EUR][1000 genomes]
rs11978816	0.96[EUR][1000 genomes]
rs11980534	0.96[EUR][1000 genomes]
rs11982889	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11984145	0.96[EUR][1000 genomes]
rs12112141	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12533808	0.81[AFR][1000 genomes]
rs1557941	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16879964	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16879966	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17171465	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17171466	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2392602	0.81[AFR][1000 genomes]
rs34753378	0.96[EUR][1000 genomes]
rs60354841	1.00[EUR][1000 genomes]
rs68175808	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6962120	0.96[EUR][1000 genomes]
rs6976100	0.96[EUR][1000 genomes]
rs713243	1.00[EUR][1000 genomes]
rs73113674	0.96[EUR][1000 genomes]
rs73113680	0.96[EUR][1000 genomes]
rs73113689	0.96[EUR][1000 genomes]
rs73113699	0.96[EUR][1000 genomes]
rs73115614	0.96[EUR][1000 genomes]
rs73115622	0.96[EUR][1000 genomes]
rs73115623	0.96[EUR][1000 genomes]
rs73115628	0.96[EUR][1000 genomes]
rs73121378	0.96[EUR][1000 genomes]
rs73121380	0.96[EUR][1000 genomes]
rs73121381	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73121384	0.96[EUR][1000 genomes]
rs73121386	0.96[EUR][1000 genomes]
rs73121396	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73121399	1.00[EUR][1000 genomes]
rs73123603	1.00[EUR][1000 genomes]
rs73123614	1.00[EUR][1000 genomes]
rs73123618	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73123621	1.00[EUR][1000 genomes]
rs73123624	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73123626	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73123893	0.92[EUR][1000 genomes]
rs73125633	0.92[EUR][1000 genomes]
rs7812184	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
rs28680843	VPS41	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:67 , 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	chr7:38839800-38871000	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr7:38847400-38869800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr7:38850600-38869600	Weak transcription	Stomach Mucosa	stomach
6	chr7:38854000-38870400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr7:38855600-38871000	Weak transcription	HepG2	liver
8	chr7:38856000-38871000	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr7:38856200-38871200	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr7:38857600-38871800	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr7:38858000-38870600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr7:38858400-38871800	Weak transcription	Lung	lung
13	chr7:38858600-38901600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr7:38858800-38907600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr7:38859000-38872800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr7:38859000-38895200	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr7:38859800-38900800	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr7:38860000-38870800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr7:38860600-38900200	Weak transcription	Fetal Intestine Large	intestine
20	chr7:38863000-38870800	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr7:38863000-38876800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr7:38863000-38888200	Weak transcription	Fetal Intestine Small	intestine
23	chr7:38863800-38879600	Weak transcription	Fetal Lung	lung
24	chr7:38864000-38870400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr7:38864000-38874000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr7:38864200-38871200	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr7:38865600-38870400	Weak transcription	Brain Cingulate Gyrus	brain
28	chr7:38865600-38873000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr7:38865800-38870000	Weak transcription	Placenta	Placenta
30	chr7:38865800-38870800	Weak transcription	Brain Anterior Caudate	brain
31	chr7:38865800-38870800	Weak transcription	Fetal Heart	heart
32	chr7:38865800-38870800	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr7:38865800-38870800	Weak transcription	Stomach Smooth Muscle	stomach
34	chr7:38865800-38871000	Weak transcription	Brain Angular Gyrus	brain
35	chr7:38865800-38871200	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr7:38865800-38872800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr7:38865800-38879600	Weak transcription	Right Atrium	heart
38	chr7:38866000-38870800	Weak transcription	Aorta	Aorta
39	chr7:38866000-38870800	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr7:38866000-38872400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr7:38866000-38886400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr7:38866400-38870400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr7:38866400-38870600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr7:38866400-38876800	Weak transcription	Primary hematopoietic stem cells	blood
45	chr7:38866400-38877000	Weak transcription	Primary T cells from cord blood	blood
46	chr7:38866800-38877000	Weak transcription	Primary B cells from cord blood	blood
47	chr7:38867200-38870200	Weak transcription	Liver	Liver
48	chr7:38867200-38871000	Weak transcription	Rectal Smooth Muscle	rectum
49	chr7:38867200-38876800	Weak transcription	Primary B cells from peripheral blood	blood
50	chr7:38867400-38869800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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