Variant report

Variant	rs34505853
Chromosome Location	chr7:38758075-38758076
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 10 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11978898	0.97[EUR][1000 genomes]
rs11983885	1.00[EUR][1000 genomes]
rs13231320	0.97[EUR][1000 genomes]
rs34165183	0.88[EUR][1000 genomes]
rs35259737	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs35360951	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35450820	0.88[EUR][1000 genomes]
rs35713809	0.88[EUR][1000 genomes]
rs73119708	0.96[EUR][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
rs34505853	VPS41	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:38749000-38803600	Weak transcription	Fetal Brain Male	brain
2	chr7:38754200-38758200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr7:38754200-38760600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr7:38754600-38759800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr7:38754600-38760800	Weak transcription	GM12878-XiMat	blood
6	chr7:38755000-38791200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr7:38755600-38760800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr7:38755800-38771600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr7:38756200-38763800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr7:38756400-38760600	Weak transcription	Primary T cells from cord blood	blood
11	chr7:38756400-38764600	Weak transcription	Fetal Brain Female	brain
12	chr7:38756800-38764800	Weak transcription	Rectal Smooth Muscle	rectum
13	chr7:38757000-38784200	Weak transcription	HMEC	breast
14	chr7:38757200-38764400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr7:38757200-38764600	Weak transcription	Primary hematopoietic stem cells	blood
16	chr7:38757200-38764600	Weak transcription	Ovary	ovary
17	chr7:38757200-38835400	Weak transcription	Psoas Muscle	Psoas
18	chr7:38757400-38760600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr7:38757400-38760600	Weak transcription	Brain Hippocampus Middle	brain
20	chr7:38757400-38764600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr7:38757600-38760200	Weak transcription	Fetal Stomach	stomach
22	chr7:38757600-38760400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr7:38757600-38760600	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr7:38757600-38760600	Weak transcription	Primary B cells from peripheral blood	blood
25	chr7:38757600-38760600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr7:38757600-38760600	Weak transcription	Adipose Nuclei	Adipose
27	chr7:38757600-38760800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr7:38757600-38761000	Weak transcription	Duodenum Mucosa	Duodenum
29	chr7:38757800-38760200	Weak transcription	Primary T cells fromperipheralblood	blood
30	chr7:38757800-38760600	Weak transcription	Brain Anterior Caudate	brain
31	chr7:38757800-38760800	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr7:38758000-38758200	Active TSS	Primary B cells from cord blood	blood
33	chr7:38758000-38760600	Weak transcription	Primary T helper cells fromperipheralblood	blood

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