Variant report

Variant	rs16879966
Chromosome Location	chr7:38843256-38843257
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1001476	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
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]
rs10951576	0.85[YRI][hapmap]
rs11970960	1.00[CEU][hapmap];0.89[YRI][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11971030	0.96[EUR][1000 genomes]
rs11977016	0.92[EUR][1000 genomes]
rs11978816	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs11980534	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs11982889	0.91[ASW][hapmap];1.00[CEU][hapmap];0.95[LWK][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11984145	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs12112141	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13231320	0.90[CEU][hapmap]
rs1557941	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16879964	1.00[CEU][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17171465	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17171466	1.00[CEU][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28680843	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34753378	0.96[EUR][1000 genomes]
rs4723792	0.89[YRI][hapmap];0.82[AFR][1000 genomes]
rs60354841	0.92[EUR][1000 genomes]
rs6415270	0.82[LWK][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes]
rs6462868	0.85[YRI][hapmap]
rs68175808	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6962120	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs6976100	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs713243	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[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	0.88[AFR][1000 genomes];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[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73121399	0.92[EUR][1000 genomes]
rs73123603	0.92[EUR][1000 genomes]
rs73123614	0.92[EUR][1000 genomes]
rs73123618	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73123621	0.92[EUR][1000 genomes]
rs73123624	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73123626	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73123893	0.92[EUR][1000 genomes]
rs73125633	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16879966	VPS41	cis	multi-tissue	Pritchard
rs16879966	VPS41	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:38793400-38861200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr7:38803200-38845400	Weak transcription	Colonic Mucosa	Colon
3	chr7:38803200-38846000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr7:38813800-38857400	Weak transcription	HSMM	muscle
5	chr7:38822400-38855200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr7:38829400-38846600	Weak transcription	Brain Anterior Caudate	brain
7	chr7:38829400-38846600	Weak transcription	Brain Substantia Nigra	brain
8	chr7:38829400-38846800	Weak transcription	Brain Cingulate Gyrus	brain
9	chr7:38829400-38854600	Weak transcription	Left Ventricle	heart
10	chr7:38829400-38855200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr7:38829400-38855600	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr7:38829400-38856400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr7:38829400-38864400	Weak transcription	Thymus	Thymus
14	chr7:38829400-38864600	Weak transcription	NHLF	lung
15	chr7:38831000-38871200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr7:38831800-38846400	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr7:38831800-38854800	Weak transcription	Fetal Stomach	stomach
18	chr7:38831800-38856800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr7:38831800-38856800	Weak transcription	Pancreas	Pancrea
20	chr7:38831800-38857000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr7:38831800-38867800	Weak transcription	Fetal Thymus	thymus
22	chr7:38832000-38846400	Weak transcription	K562	blood
23	chr7:38832000-38855600	Weak transcription	Dnd41	blood
24	chr7:38832000-38857400	Weak transcription	Lung	lung
25	chr7:38832400-38855200	Weak transcription	Fetal Intestine Small	intestine
26	chr7:38832800-38857000	Weak transcription	Esophagus	oesophagus
27	chr7:38833400-38846800	Weak transcription	Brain Angular Gyrus	brain
28	chr7:38833400-38857000	Weak transcription	Duodenum Mucosa	Duodenum
29	chr7:38833400-38859400	Weak transcription	Spleen	Spleen
30	chr7:38833600-38857000	Weak transcription	Aorta	Aorta
31	chr7:38833600-38857200	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr7:38834400-38847200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr7:38834400-38863400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr7:38834600-38853600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr7:38835000-38844200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr7:38835200-38855200	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr7:38835200-38855600	Weak transcription	Fetal Intestine Large	intestine
38	chr7:38835200-38857000	Weak transcription	Fetal Lung	lung
39	chr7:38835200-38865200	Weak transcription	Rectal Smooth Muscle	rectum
40	chr7:38835400-38844000	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr7:38835400-38846600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr7:38835400-38854000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr7:38835400-38855200	Weak transcription	Liver	Liver
44	chr7:38835400-38857000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr7:38835600-38856400	Weak transcription	Stomach Smooth Muscle	stomach
46	chr7:38835600-38857400	Weak transcription	Ovary	ovary
47	chr7:38835600-38857600	Weak transcription	Adipose Nuclei	Adipose
48	chr7:38835600-38862200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr7:38835600-38900800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr7:38835800-38855600	Weak transcription	HSMMtube	muscle

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