Variant report

Variant	rs11984145
Chromosome Location	chr7:38835035-38835036
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1001476	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs10486680	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs10951573	0.90[CEU][hapmap]
rs11970960	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs11971030	1.00[EUR][1000 genomes]
rs11977016	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11978816	1.00[CEU][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11980534	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11982889	1.00[CEU][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs12112141	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs13231320	0.90[CEU][hapmap]
rs1557941	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs16879964	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs16879966	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs17171465	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs17171466	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs28680843	0.96[EUR][1000 genomes]
rs34753378	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60354841	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs68175808	1.00[EUR][1000 genomes]
rs6962120	1.00[CEU][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6976100	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs713243	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]
rs73113674	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73113680	1.00[EUR][1000 genomes]
rs73113689	1.00[EUR][1000 genomes]
rs73113699	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73115614	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73115622	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73115623	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73115628	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73121378	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73121380	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73121381	1.00[EUR][1000 genomes]
rs73121384	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73121386	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73121396	0.96[EUR][1000 genomes]
rs73121399	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73123603	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73123614	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73123618	0.96[EUR][1000 genomes]
rs73123621	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73123624	0.96[EUR][1000 genomes]
rs73123626	0.96[EUR][1000 genomes]
rs73123893	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73125633	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7812184	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[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

Variant related diseases (count:1)

Disease	PMID	Source
Cognitive performance	19734545	GWAS catalog

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11984145	VPS41	cis	multi-tissue	Pritchard
rs11984145	VPS41	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:38757200-38835400	Weak transcription	Psoas Muscle	Psoas
2	chr7:38793400-38861200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr7:38800200-38837600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr7:38803200-38845400	Weak transcription	Colonic Mucosa	Colon
5	chr7:38803200-38846000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr7:38804400-38836200	Weak transcription	Fetal Brain Male	brain
7	chr7:38813800-38836400	Weak transcription	HUVEC	blood vessel
8	chr7:38813800-38839600	Weak transcription	Right Ventricle	heart
9	chr7:38813800-38857400	Weak transcription	HSMM	muscle
10	chr7:38820000-38836600	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr7:38822200-38837400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr7:38822400-38836400	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr7:38822400-38855200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr7:38823600-38835400	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr7:38824800-38836400	Strong transcription	Primary B cells from cord blood	blood
16	chr7:38825000-38837800	Weak transcription	Fetal Heart	heart
17	chr7:38825200-38836400	Strong transcription	Primary B cells from peripheral blood	blood
18	chr7:38825600-38835800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr7:38825600-38835800	Strong transcription	GM12878-XiMat	blood
20	chr7:38825800-38835600	Strong transcription	Adipose Nuclei	Adipose
21	chr7:38825800-38836000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr7:38826200-38836400	Strong transcription	Primary T helper cells fromperipheralblood	blood
23	chr7:38827000-38836200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr7:38827200-38836400	Strong transcription	Rectal Mucosa Donor 29	rectum
25	chr7:38827400-38836400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr7:38827600-38835400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr7:38827600-38835800	Strong transcription	Primary T cells fromperipheralblood	blood
28	chr7:38828200-38836200	Strong transcription	Primary neutrophils fromperipheralblood	blood
29	chr7:38828400-38835400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr7:38828600-38835400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr7:38828600-38836400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr7:38829200-38837200	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr7:38829400-38835200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr7:38829400-38836000	Weak transcription	Fetal Brain Female	brain
35	chr7:38829400-38836200	Weak transcription	Fetal Kidney	kidney
36	chr7:38829400-38836200	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr7:38829400-38836400	Weak transcription	Brain Hippocampus Middle	brain
38	chr7:38829400-38837200	Weak transcription	Small Intestine	intestine
39	chr7:38829400-38837400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr7:38829400-38837600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr7:38829400-38837600	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr7:38829400-38838200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr7:38829400-38839000	Weak transcription	Gastric	stomach
44	chr7:38829400-38841600	Weak transcription	Osteobl	bone
45	chr7:38829400-38846600	Weak transcription	Brain Anterior Caudate	brain
46	chr7:38829400-38846600	Weak transcription	Brain Substantia Nigra	brain
47	chr7:38829400-38846800	Weak transcription	Brain Cingulate Gyrus	brain
48	chr7:38829400-38854600	Weak transcription	Left Ventricle	heart
49	chr7:38829400-38855200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr7:38829400-38855600	Weak transcription	Skeletal Muscle Male	skeletal muscle

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